#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IGV	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
CFAP74	85452	bcgsc.ca;mdanderson.org	37	1	1855319	1855319	+	IGR	SNP	C	C	T	rs2295362	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:1855319C>T								TMEM52 (4607 upstream) : C1orf222 (64243 downstream)																							CCATGACGCCCTTGACGGGGG	0.597													C|||	1161	0.231829	0.4864	0.0735	5008	,	,		11367	0.1577		0.0447	False		,,,				2504	0.2689				.													.	.			0			.							C		1657,2747	504.1+/-365.7	300,1057,845	146.0	134.0	138.0		282	-0.6	0.1	1	dbSNP_100	138	344,8256	115.9+/-175.7	6,332,3962	no	coding-synonymous	C1orf222	XM_003403417.1		306,1389,4807	TT,TC,CC		4.0,37.6249,15.3876		94/306	1855319	2001,11003	2202	4300	6502	SO:0001628	intergenic_variant	339457	.			GACGCCCTTGACG																													1.37:g.1855319C>T			123	0	0		110	0.10	11	.	0		0		Silent	SNP		37																																																																																					0	0.597										
CFAP74	85452	bcgsc.ca;mdanderson.org	37	1	1858161	1858161	+	IGR	SNP	C	C	T	rs78807865	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:1858161C>T								TMEM52 (7449 upstream) : C1orf222 (61401 downstream)																							ATGGTGCCACCGTCGGGCACC	0.652													C|||	1206	0.240815	0.4992	0.1124	5008	,	,		15902	0.1597		0.0437	False		,,,				2504	0.2689				.													.	.			0			.																																									SO:0001628	intergenic_variant	339457	.			TGCCACCGTCGGG																													1.37:g.1858161C>T			257	0	0		212	0.08	17	.	0		0		Silent	SNP		37																																																																																					0	0.652										
C1orf167	284498	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11835556	11835556	+	Missense_Mutation	SNP	C	C	T	rs41275456	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11835556C>T	ENST00000433342.1	+	9	2125	c.2125C>T	c.(2125-2127)Cgc>Tgc	p.R709C	C1orf167_ENST00000484153.1_3'UTR|RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	709										central_nervous_system(1)	1						CCTGGCTGACCGCCGGACGGG	0.622													C|||	649	0.129593	0.1362	0.0576	5008	,	,		17905	0.1141		0.1034	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001583	missense	284498	.			GCTGACCGCCGGA	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2125C>T	1.37:g.11835556C>T	ENSP00000414909:p.Arg709Cys		222	0	0		183	0.13	24	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		213|213	0.09752747252747253|0.09752747252747253	58|58	0.11788617886178862|0.11788617886178862	20|20	0.055248618784530384|0.055248618784530384	56|56	0.0979020979020979|0.0979020979020979	79|79	0.10422163588390501|0.10422163588390501	C|C	20.5|20.5	3.992695|3.992695	0.74703|0.74703	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000312793|ENST00000433342	.|T	.|0.07327	.|3.2	4.76|4.76	0.555|0.555	0.17247|0.17247	.|.	.|.	.|.	.|.	.|.	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34900|0.34900	-0.9810|-0.9810	4|6	.|0.87932	.|D	.|0	.|.	6.0137|6.0137	0.19589|0.19589	0.0:0.5338:0.0:0.4662|0.0:0.5338:0.0:0.4662	rs41275456|rs41275456	.|.	.|.	.|.	L|C	68|709	.|ENSP00000414909:R709C	.|ENSP00000414909:R709C	P|R	+|+	2|1	0|0	C1orf167|C1orf167	11758143|11758143	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.575000|0.575000	0.36095|0.36095	-0.801000|-0.801000	0.04550|0.04550	0.246000|0.246000	0.21394|0.21394	0.462000|0.462000	0.41574|0.41574	CCG|CGC			0.622	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11836670	11836670	+	Silent	SNP	C	C	A	rs41275458	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11836670C>A	ENST00000433342.1	+	10	2386	c.2386C>A	c.(2386-2388)Cgg>Agg	p.R796R	C1orf167_ENST00000484153.1_3'UTR|RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	796										central_nervous_system(1)	1						GTGGAAGATGCGGCTTTTCCA	0.682													C|||	650	0.129792	0.1369	0.0576	5008	,	,		16684	0.1141		0.1034	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001819	synonymous_variant	284498	.			AAGATGCGGCTTT	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2386C>A	1.37:g.11836670C>A			257	0	0		214	0.12	26	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		213	0.09752747252747253	58	0.11788617886178862	20	0.055248618784530384	56	0.0979020979020979	79	0.10422163588390501	C	4.415	0.076782	0.08485	.	.	ENSG00000215910	ENST00000312793	.	.	.	4.65	-2.84	0.05751	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.20472	-1.0274	3	.	.	.	-16.4485	3.98	0.09490	0.5551:0.2321:0.1263:0.0866	rs41275458	.	.	.	E	155	.	.	A	+	2	0	C1orf167	11759257	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.030000	0.03581	-0.305000	0.08831	-0.263000	0.10527	GCG			0.682	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca;mdanderson.org	37	1	11838762	11838762	+	Silent	SNP	G	G	A	rs72640211	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11838762G>A	ENST00000433342.1	+	11	2457	c.2457G>A	c.(2455-2457)ctG>ctA	p.L819L	RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	819										central_nervous_system(1)	1						AGCGCAGCCTGAGATGGTGGC	0.637													G|||	166	0.033147	0.0303	0.0101	5008	,	,		16021	0.002		0.0686	False		,,,				2504	0.0491				.													.	.			0			.																																									SO:0001819	synonymous_variant	284498	.			CAGCCTGAGATGG	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2457G>A	1.37:g.11838762G>A			257	0	0		173	0.06	11	.	0		0	Q8NDA9|Q8NDF3	Silent	SNP	ENST00000433342.1	37		68	0.031135531135531136	16	0.032520325203252036	1	0.0027624309392265192	1	0.0017482517482517483	50	0.06596306068601583	G	8.370	0.835203	0.16820	.	.	ENSG00000215910	ENST00000312793	.	.	.	4.69	2.72	0.32119	.	.	.	.	.	T	0.02767	0.0083	.	.	.	0.23221	N	0.99809	.	.	.	.	.	.	T	0.06752	-1.0809	4	.	.	.	-2.368	6.8252	0.23878	0.1022:0.1964:0.7013:0.0	.	.	.	.	K	179	.	.	E	+	1	0	C1orf167	11761349	0.747000	0.28283	0.016000	0.15963	0.006000	0.05464	1.348000	0.33987	0.452000	0.26830	0.514000	0.50259	GAG			0.637	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca;mdanderson.org	37	1	11838841	11838841	+	Missense_Mutation	SNP	A	A	G	rs56001051	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11838841A>G	ENST00000433342.1	+	11	2536	c.2536A>G	c.(2536-2538)Agc>Ggc	p.S846G	RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	846										central_nervous_system(1)	1						GGAGCCACTGAGCAGCAGCAC	0.637													G|||	650	0.129792	0.1369	0.0576	5008	,	,		15451	0.1141		0.1034	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001583	missense	284498	.			CCACTGAGCAGCA	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2536A>G	1.37:g.11838841A>G	ENSP00000414909:p.Ser846Gly		321	0.0031152648	1		267	0.07	20	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		213|213	0.09752747252747253|0.09752747252747253	58|58	0.11788617886178862|0.11788617886178862	20|20	0.055248618784530384|0.055248618784530384	56|56	0.0979020979020979|0.0979020979020979	79|79	0.10422163588390501|0.10422163588390501	G|G	8.139|8.139	0.784776|0.784776	0.16189|0.16189	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000312793|ENST00000433342	.|T	.|0.04758	.|3.56	4.55|4.55	2.6|2.6	0.31112|0.31112	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.46652|0.46652	-0.9176|-0.9176	4|7	.|.	.|.	.|.	2.2558|2.2558	4.927|4.927	0.13898|0.13898	0.1994:0.1743:0.6263:0.0|0.1994:0.1743:0.6263:0.0	rs56001051|rs56001051	.|846	.|Q5SNV9	.|CA167_HUMAN	G|G	205|846	.|ENSP00000414909:S846G	.|.	E|S	+|+	2|1	0|0	C1orf167|C1orf167	11761428|11761428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.178000|-0.178000	0.09782|0.09782	0.104000|0.104000	0.17725|0.17725	-0.479000|-0.479000	0.04858|0.04858	GAG|AGC			0.637	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca;mdanderson.org	37	1	11839009	11839009	+	Silent	SNP	C	C	T	rs55685198	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11839009C>T	ENST00000433342.1	+	12	2595	c.2595C>T	c.(2593-2595)gaC>gaT	p.D865D	RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	865										central_nervous_system(1)	1						CCCTCCCGGACACTCTCCAGG	0.672													T|||	650	0.129792	0.1369	0.0576	5008	,	,		14528	0.1141		0.1034	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001819	synonymous_variant	284498	.			CCCGGACACTCTC	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2595C>T	1.37:g.11839009C>T			215	0	0		165	0.08	13	.	0		0	Q8NDA9|Q8NDF3	Silent	SNP	ENST00000433342.1	37		213	0.09752747252747253	58	0.11788617886178862	20	0.055248618784530384	56	0.0979020979020979	79	0.10422163588390501	T	3.168	-0.170556	0.06421	.	.	ENSG00000215910	ENST00000312793;ENST00000444493	.	.	.	4.85	1.67	0.24075	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.11446	-1.0587	3	.	.	.	-7.0561	7.7598	0.28946	0.0:0.2908:0.4046:0.3046	rs55685198	.	.	.	Y	225;8	.	.	H	+	1	0	C1orf167	11761596	0.045000	0.20229	0.037000	0.18230	0.007000	0.05969	-0.030000	0.12308	0.117000	0.18138	-2.682000	0.00141	CAC			0.672	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca	37	1	11839034	11839034	+	Missense_Mutation	SNP	G	G	A	rs55967531	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:11839034G>A	ENST00000433342.1	+	12	2620	c.2620G>A	c.(2620-2622)Gca>Aca	p.A874T	RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	874										central_nervous_system(1)	1						CCTTCTGTGGGCAGCTGGGCA	0.682													G|||	583	0.116414	0.0877	0.0548	5008	,	,		14905	0.1141		0.1034	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001583	missense	284498	.			CTGTGGGCAGCTG	AL834308		1p36.22	2012-04-20			ENSG00000215910	ENSG00000215910			25262	protein-coding gene	gene with protein product						12370778	Standard	XM_006710065		Approved	DKFZp434E1410, RP11-56N19.2	uc001asy.1	Q5SNV9	OTTHUMG00000002228	ENST00000433342.1:c.2620G>A	1.37:g.11839034G>A	ENSP00000414909:p.Ala874Thr		192	0	0		135	0.06	8	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		197|197	0.0902014652014652|0.0902014652014652	44|44	0.08943089430894309|0.08943089430894309	18|18	0.049723756906077346|0.049723756906077346	56|56	0.0979020979020979|0.0979020979020979	79|79	0.10422163588390501|0.10422163588390501	G|G	14.69|14.69	2.610833|2.610833	0.46527|0.46527	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000433342|ENST00000312793;ENST00000444493	T|.	0.05513|.	3.43|.	4.85|4.85	2.91|2.91	0.33838|0.33838	.|.	1.505680|.	0.04983|.	N|.	0.466035|.	T|T	0.00637|0.00637	0.0021|0.0021	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	P|.	0.50943|.	0.94|.	P|.	0.47981|.	0.563|.	T|T	0.16188|0.16188	-1.0411|-1.0411	9|4	0.48119|.	T|.	0.1|.	-0.0202|-0.0202	7.1653|7.1653	0.25687|0.25687	0.0964:0.171:0.7326:0.0|0.0964:0.171:0.7326:0.0	rs55967531|rs55967531	874|.	Q5SNV9|.	CA167_HUMAN|.	T|D	874|233;16	ENSP00000414909:A874T|.	ENSP00000414909:A874T|.	A|G	+|+	1|2	0|0	C1orf167|C1orf167	11761621|11761621	0.010000|0.010000	0.17322|0.17322	0.073000|0.073000	0.20177|0.20177	0.210000|0.210000	0.24377|0.24377	0.336000|0.336000	0.19823|0.19823	0.437000|0.437000	0.26423|0.26423	0.400000|0.400000	0.26472|0.26472	GCA|GGC			0.682	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
PRAMEF30P	441870	bcgsc.ca	37	1	12898045	12898045	+	IGR	SNP	G	G	A	rs10158988	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:12898045G>A								PRAMEF11 (6781 upstream) : HNRNPCL1 (9215 downstream)																							GGGTGGGACCGAAGAAGATCC	0.552													.|||	2498	0.498802	0.7352	0.402	5008	,	,		8959	0.4018		0.3549	False		,,,				2504	0.4959				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGACCGAAGAAG																													1.37:g.12898045G>A			82	0	0		63	0.29	18	.	0		0		RNA	SNP		37																																																																																					0	0.552										
PRAMEF30P	441870	bcgsc.ca	37	1	12898647	12898647	+	IGR	SNP	C	C	T	rs149631941	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:12898647C>T								PRAMEF11 (7383 upstream) : HNRNPCL1 (8613 downstream)																							CAACTTTCTCCAGCAGAACTC	0.562													.|||	445	0.0888578	0.0658	0.0994	5008	,	,		15008	0.1111		0.1123	False		,,,				2504	0.0654				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTCTCCAGCAGA																													1.37:g.12898647C>T			99	0.0101010101	1		72	0.11	8	.	0		0		RNA	SNP		37																																																																																					0	0.562										
PRAMEF7	441871	bcgsc.ca;mdanderson.org	37	1	12979729	12979729	+	Silent	SNP	G	G	A	rs146836223		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:12979729G>A	ENST00000361079.2	+	4	1004	c.921G>A	c.(919-921)tcG>tcA	p.S307S	RNU6-1072P_ENST00000384703.1_RNA			Q5VXH5	PRAM7_HUMAN	PRAME family member 7	307					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCAGAGTCGGACTTGAAGC	0.567																																					p.S307S													.	.			0			c.G921A												19.0	16.0	17.0					1																	12979729		1528	3202	4730	SO:0001819	synonymous_variant	441871	exon4			AGAGTCGGACTTG		CCDS30593.1	1p36.21	2013-01-17			ENSG00000204510	ENSG00000204510		"""-"""	28415	protein-coding gene	gene with protein product							Standard	NM_001012277		Approved			Q5VXH5	OTTHUMG00000001982	ENST00000361079.2:c.921G>A	1.37:g.12979729G>A			331	0	0		298	0.06	17	NM_001012276	0		0	B9EIP0	Silent	SNP	ENST00000361079.2	37	CCDS30593.1																																																																																					0.567	PRAMEF7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001012277	
PRAMEF7	441871	bcgsc.ca;mdanderson.org	37	1	12979845	12979845	+	Missense_Mutation	SNP	T	T	C	rs1890765	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:12979845T>C	ENST00000361079.2	+	4	1120	c.1037T>C	c.(1036-1038)gTt>gCt	p.V346A	RNU6-1072P_ENST00000384703.1_RNA			Q5VXH5	PRAM7_HUMAN	PRAME family member 7	346					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGAGCAAGTTGTGGCCACC	0.602																																					p.V346A													.	.			0			c.T1037C							T	ALA/VAL	379,4021		0,379,1821	52.0	48.0	49.0		1037	-0.9	0.0	1	dbSNP_134	49	1970,6602		26,1918,2342	no	missense	PRAMEF7	NM_001012277.1	64	26,2297,4163	CC,CT,TT		22.9818,8.6136,18.1082	benign	346/475	12979845	2349,10623	2200	4286	6486	SO:0001583	missense	441871	exon4			AGCAAGTTGTGGC		CCDS30593.1	1p36.21	2013-01-17			ENSG00000204510	ENSG00000204510		"""-"""	28415	protein-coding gene	gene with protein product							Standard	NM_001012277		Approved			Q5VXH5	OTTHUMG00000001982	ENST00000361079.2:c.1037T>C	1.37:g.12979845T>C	ENSP00000354371:p.Val346Ala		653	0	0		587	0.10	58	NM_001012276	0		0	B9EIP0	Missense_Mutation	SNP	ENST00000361079.2	37	CCDS30593.1	.	.	.	.	.	.	.	.	.	.	.	2.115	-0.402770	0.04865	0.086136	0.229818	ENSG00000204510	ENST00000361079;ENST00000330881	T;T	0.14893	2.47;2.47	1.68	-0.877	0.10621	.	0.876931	0.09824	N	0.751126	T	0.00012	0.0000	L	0.42008	1.315	0.09310	N	1	B	0.20261	0.043	B	0.21360	0.034	T	0.41645	-0.9497	10	0.44086	T	0.13	.	5.3826	0.16199	0.0:0.3266:0.0:0.6734	.	346	Q5VXH5	PRAM7_HUMAN	A	346	ENSP00000354371:V346A;ENSP00000328915:V346A	ENSP00000328915:V346A	V	+	2	0	PRAMEF7	12902432	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	0.068000	0.14531	-0.242000	0.09667	-0.850000	0.03035	GTT			0.602	PRAMEF7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001012277	
PRAMEF7	441871	bcgsc.ca;mdanderson.org	37	1	12980150	12980150	+	Missense_Mutation	SNP	A	A	G	rs113065075	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:12980150A>G	ENST00000361079.2	+	4	1425	c.1342A>G	c.(1342-1344)Atc>Gtc	p.I448V	RNU6-1072P_ENST00000384703.1_RNA			Q5VXH5	PRAM7_HUMAN	PRAME family member 7	448					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					endometrium(2)|kidney(5)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)	18	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGCCCAAGATCATTGTGTT	0.577													a|||	377	0.0752796	0.0129	0.1153	5008	,	,		14679	0.0188		0.1302	False		,,,				2504	0.1329				p.I448V													.	.			0			c.A1342G							A	VAL/ILE	128,3544		38,52,1746	86.0	84.0	85.0		1342	0.5	0.0	1	dbSNP_134	85	1206,6242		382,442,2900	no	missense	PRAMEF7	NM_001012277.1	29	420,494,4646	GG,GA,AA		16.1923,3.4858,11.9964	benign	448/475	12980150	1334,9786	1836	3724	5560	SO:0001583	missense	441871	exon4			CCCAAGATCATTG		CCDS30593.1	1p36.21	2013-01-17			ENSG00000204510	ENSG00000204510		"""-"""	28415	protein-coding gene	gene with protein product							Standard	NM_001012277		Approved			Q5VXH5	OTTHUMG00000001982	ENST00000361079.2:c.1342A>G	1.37:g.12980150A>G	ENSP00000354371:p.Ile448Val		305	0	0		192	0.18	34	NM_001012276	0		0	B9EIP0	Missense_Mutation	SNP	ENST00000361079.2	37	CCDS30593.1	114	0.0521978021978022	5	0.01016260162601626	28	0.07734806629834254	6	0.01048951048951049	75	0.09894459102902374	.	0.013	-1.613353	0.00835	0.034858	0.161923	ENSG00000204510	ENST00000361079;ENST00000330881	T;T	0.46451	0.87;0.87	1.68	0.495	0.16890	.	2.160190	0.02169	N	0.059557	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B	0.23316	0.083	B	0.21151	0.033	T	0.06862	-1.0803	10	0.22706	T	0.39	.	3.5692	0.07910	0.7802:0.0:0.2198:0.0	.	448	Q5VXH5	PRAM7_HUMAN	V	448	ENSP00000354371:I448V;ENSP00000328915:I448V	ENSP00000328915:I448V	I	+	1	0	PRAMEF7	12902737	0.000000	0.05858	0.001000	0.08648	0.061000	0.15899	0.121000	0.15667	0.121000	0.18284	0.254000	0.18369	ATC			0.577	PRAMEF7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001012277	
KAZN	23254	hgsc.bcm.edu	37	1	15439098	15439098	+	Intron	SNP	C	C	T	rs114844404		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:15439098C>T	ENST00000376030.2	+	14	2457					NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein						keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CTTTTTTTCTCCTCCCGGGAG	0.587																																					.													.	.			0			.																																									SO:0001627	intron_variant	200197	.			TTTTCTCCTCCCG	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2163+61C>T	1.37:g.15439098C>T			104	0	0		103	0.19	20	.	1	0.00	0	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	RNA	SNP	ENST00000376030.2	37	CCDS152.2																																																																																					0.587	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000005690.2		NM_001017999	
ESPNP	284729	broad.mit.edu	37	1	17030903	17030905	+	RNA	DEL	GAG	GAG	-	rs67156338|rs376609585	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GAG	GAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:17030903_17030905delGAG	ENST00000492551.1	-	0	696					NR_026567.1				espin pseudogene																		AGAGATCGACGAGGAGGGGGCCT	0.64														1867	0.372804	0.3245	0.3343	5008	,	,		43669	0.4474		0.3936	False		,,,				2504	0.3671				.													.	.			0			.																																											0	.			ATCGACGAGGAGG	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17030906_17030908delGAG			8	0	0		6	0.50	3	.	0		0		RNA	DEL	ENST00000492551.1	37																																																																																						0.640	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000326311.1			
PADI6	353238	broad.mit.edu	37	1	17723476	17723477	+	RNA	INS	-	-	CA	rs397791237|rs367811358|rs561097279|rs61476146	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:17723476_17723477insCA	ENST00000434762.2	+	0	1669							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AGGAATGCACCCAGGTGGCTGG	0.629														1693	0.338059	0.4024	0.3689	5008	,	,		20008	0.1716		0.3728	False		,,,				2504	0.365				.													.	PADI6	51		0			.																																											353238	.			ATGCACCCAGGTG	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17723477_17723478dupCA			108	0	0		95	0.07	7	.	0		0	Q330K5|Q70SX3	RNA	INS	ENST00000434762.2	37																																																																																						0.629	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000006804.4		NM_207421	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808340	18808340	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:18808340G>T	ENST00000400664.1	+	1	917	c.865G>T	c.(865-867)Gtg>Ttg	p.V289L		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	289						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CAAGGGCAAGGTGTACGACTA	0.592																																					p.V289L													.	.			0			c.G865T												82.0	79.0	80.0					1																	18808340		2203	4300	6503	SO:0001583	missense	127707	exon1			GGCAAGGTGTACG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.865G>T	1.37:g.18808340G>T	ENSP00000383505:p.Val289Leu		139	0	0		122	0.05	6	NM_152375	0		0	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	.	.	.	.	.	.	.	.	.	.	G	11.88	1.769164	0.31320	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.79352	-1.26	5.02	1.6	0.23607	.	1.073350	0.07292	U	0.872634	T	0.61223	0.2330	L	0.27053	0.805	0.30360	N	0.783947	P;P	0.43287	0.802;0.802	B;B	0.34489	0.184;0.184	T	0.60016	-0.7345	10	0.72032	D	0.01	.	5.1974	0.15245	0.3183:0.156:0.5257:0.0	.	226;289	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	L	289;226	ENSP00000383505:V289L	ENSP00000383505:V289L	V	+	1	0	KLHDC7A	18680927	1.000000	0.71417	0.894000	0.35097	0.069000	0.16628	3.151000	0.50670	0.490000	0.27771	0.313000	0.20887	GTG			0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000006923.3		NM_152375	
Unknown	0	bcgsc.ca	37	1	21738259	21738259	+	IGR	SNP	C	C	T	rs35836191	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:21738259C>T								ECE1 (66262 upstream) : RP11-293F5.1 (4131 downstream)																							TTTGAATGACCTTGTTGGCAT	0.483													c|||	314	0.0626997	0.1006	0.0605	5008	,	,		21205	0.001		0.1014	False		,,,				2504	0.0368				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AATGACCTTGTTG																													1.37:g.21738259C>T			48	0	0		35	0.11	4	.	0		0		RNA	SNP		37																																																																																					0	0.483										
HSPG2	3339	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	22202476	22202476	+	Silent	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:22202476G>A	ENST00000374695.3	-	24	3142	c.3063C>T	c.(3061-3063)tcC>tcT	p.S1021S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1021	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAGGGGTGTGGAGCCCGGCT	0.637																																					p.S1021S													.	.			0			c.C3063T												55.0	60.0	58.0					1																	22202476		2203	4300	6503	SO:0001819	synonymous_variant	3339	exon24			GGGTGTGGAGCCC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3063C>T	1.37:g.22202476G>A			94	0	0		107	0.07	8	NM_005529	142	0.07	10	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																					0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000007598.1		NM_005529	
CSMD2	114784	bcgsc.ca	37	1	33999430	33999430	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:33999430G>T	ENST00000373381.4	-	63	10133	c.9957C>A	c.(9955-9957)aaC>aaA	p.N3319K		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCCAGGTCAGGTTTGGGAGGC	0.562																																					p.N3175K													.	CSMD2	946		0			c.C9525A												142.0	120.0	128.0					1																	33999430		2203	4300	6503	SO:0001583	missense	114784	exon62			GGTCAGGTTTGGG	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9957C>A	1.37:g.33999430G>T	ENSP00000362479:p.Asn3319Lys		154	0	0		155	0.04	6	NM_052896	0		0	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.067158	0.76301	.	.	ENSG00000121904	ENST00000373381	T	0.67523	-0.27	5.33	5.33	0.75918	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.82508	0.5052	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.84538	0.0637	10	0.59425	D	0.04	.	11.4773	0.50306	0.0821:0.0:0.9179:0.0	.	3175;3319	Q7Z408;E7EUA6	CSMD2_HUMAN;.	K	3319	ENSP00000362479:N3319K	ENSP00000241312:N3175K	N	-	3	2	CSMD2	33772017	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.974000	0.49272	2.505000	0.84491	0.591000	0.81541	AAC			0.562	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_052896	
ADH5P2	343296	bcgsc.ca	37	1	79987731	79987731	+	IGR	SNP	G	G	A	rs140314886	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:79987731G>A								RP4-726F1.1 (197183 upstream) : RP11-339A11.2 (592896 downstream)																							GCCATTGGAGGATGGAAGAGT	0.428													G|||	31	0.0061901	0.0008	0.0144	5008	,	,		20922	0.0		0.0199	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	343296	.			TTGGAGGATGGAA																													1.37:g.79987731G>A			149	0	0		150	0.07	11	.	0		0		RNA	SNP		37																																																																																					0	0.428										
Unknown	0	bcgsc.ca	37	1	100797449	100797449	+	IGR	SNP	A	A	T	rs614766	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:100797449A>T								RTCA (39124 upstream) : RP5-837M10.2 (12583 downstream)																							AACAAAGGCCATCACGCCATT	0.318													A|||	3134	0.625799	0.9281	0.464	5008	,	,		19780	0.4623		0.5388	False		,,,				2504	0.59				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGGCCATCACGC																													1.37:g.100797449A>T			258	0	0		185	0.04	7	.	0		0		RNA	SNP		37																																																																																					0	0.318										
LOC100129138	100129138	bcgsc.ca	37	1	104615959	104615959	+	lincRNA	SNP	A	A	G	rs3811506	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:104615959A>G	ENST00000418362.1	+	0	315					NR_033990.1																						CCCGACAAGCAGCCATCTGAT	0.552													A|||	1385	0.276558	0.2224	0.3617	5008	,	,		15125	0.5308		0.1173	False		,,,				2504	0.1912				.													.	.			0			.																																											0	.			ACAAGCAGCCATC																													1.37:g.104615959A>G			168	0	0		124	0.06	7	.	5	0.00	0		RNA	SNP	ENST00000418362.1	37																																																																																						0.552	RP11-364B6.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000030377.1			
CNOT7P2	100132332	bcgsc.ca	37	1	116107337	116107337	+	IGR	SNP	T	T	A	rs41441746	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:116107337T>A								AL512638.1 (78973 upstream) : RN7SL420P (41754 downstream)																							GTTGCTATGGTCACCGAGTTT	0.398													A|||	1231	0.245807	0.0915	0.2378	5008	,	,		18877	0.3323		0.172	False		,,,				2504	0.4468				.													.	.			0			.																																									SO:0001628	intergenic_variant	100132332	.			CTATGGTCACCGA																													1.37:g.116107337T>A			73	0	0		58	0.14	8	.	0		0		RNA	SNP		37																																																																																					0	0.398										
HNRNPA1P43	400769	bcgsc.ca	37	1	116400426	116400426	+	IGR	SNP	T	T	C	rs7512945	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:116400426T>C								NHLH2 (13888 upstream) : RP11-12L8.1 (61570 downstream)																							CTTTAGGAGATTCTGACTTAG	0.468													C|||	1118	0.223243	0.3986	0.1196	5008	,	,		19515	0.1984		0.1899	False		,,,				2504	0.1196				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGAGATTCTGAC																													1.37:g.116400426T>C			40	0	0		23	0.17	4	.	0		0		RNA	SNP		37																																																																																					0	0.468										
NBPF10	100132406	bcgsc.ca;mdanderson.org	37	1	145365372	145365372	+	Missense_Mutation	SNP	C	C	G	rs4126496	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:145365372C>G	ENST00000342960.5	+	80	10032	c.9997C>G	c.(9997-9999)Ctt>Gtt	p.L3333V	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	647						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTCAGGTTGTCTTGAACTGTG	0.488													.|||	1218	0.243211	0.1377	0.3674	5008	,	,		33448	0.1627		0.3887	False		,,,				2504	0.2311				p.L3333V													.	NBPF10	221		0			c.C9997G																																									SO:0001583	missense	100132406	exon80			GGTTGTCTTGAAC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.9997C>G	1.37:g.145365372C>G	ENSP00000345684:p.Leu3333Val		108	0	0		97	0.11	11	NM_001039703	14	0.00	0	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	7.899	0.734062	0.15574	.	.	ENSG00000163386	ENST00000342960	T	0.07216	3.21	0.74	0.74	0.18330	.	.	.	.	.	T	0.02193	0.0068	L	0.36672	1.1	0.80722	P	0.0	.	.	.	.	.	.	T	0.47262	-0.9131	6	0.17369	T	0.5	.	4.8933	0.13737	0.0:1.0:0.0:0.0	rs4126496	.	.	.	V	3333	ENSP00000345684:L3333V	ENSP00000345684:L3333V	L	+	1	0	NBPF10	144076729	0.002000	0.14202	0.001000	0.08648	0.018000	0.09664	1.024000	0.30077	0.725000	0.32318	0.152000	0.16155	CTT			0.488	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_001039703	
LOC728989	728989	bcgsc.ca	37	1	146522606	146522606	+	IGR	SNP	T	T	C	rs521687	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146522606T>C								RP4-704D21.2 (47429 upstream) : RNVU1-8 (28688 downstream)																							ACTCAGTCTCTAAAAAGCTAA	0.478													.|||	1918	0.382987	0.4039	0.4179	5008	,	,		15814	0.4335		0.2237	False		,,,				2504	0.4417				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTCTCTAAAAAG																													1.37:g.146522606T>C			178	0	0		151	0.15	23	.	14	0.00	0		RNA	SNP		37																																																																																					0	0.478										
LOC728989	728989	bcgsc.ca	37	1	146522686	146522686	+	IGR	SNP	C	C	T	rs522558	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146522686C>T								RP4-704D21.2 (47509 upstream) : RNVU1-8 (28608 downstream)																							GGACTTTTGGCTCAATATGGA	0.418													.|||	1688	0.337061	0.2943	0.4049	5008	,	,		16924	0.3909		0.2018	False		,,,				2504	0.4305				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTGGCTCAATA																													1.37:g.146522686C>T			105	0	0		95	0.07	7	.	27	0.00	0		RNA	SNP		37																																																																																					0	0.418										
LOC728989	728989	bcgsc.ca	37	1	146522722	146522722	+	IGR	SNP	T	T	C	rs671205	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146522722T>C								RP4-704D21.2 (47545 upstream) : RNVU1-8 (28572 downstream)																							GAACAACAAGTCAACACAGAC	0.443													.|||	1801	0.359625	0.3079	0.4135	5008	,	,		18273	0.4425		0.2217	False		,,,				2504	0.4479				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AACAAGTCAACAC																													1.37:g.146522722T>C			100	0	0		92	0.08	7	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.443										
LOC728989	728989	bcgsc.ca	37	1	146523665	146523665	+	IGR	SNP	G	G	A	rs61997227	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146523665G>A								RP4-704D21.2 (48488 upstream) : RNVU1-8 (27629 downstream)																							TCAACGAAAGGATGGTCATCA	0.532													.|||	93	0.0185703	0.0015	0.0317	5008	,	,		19700	0.004		0.0537	False		,,,				2504	0.0112				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGAAAGGATGGTC																													1.37:g.146523665G>A			48	0	0		63	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.532										
LOC728989	728989	bcgsc.ca	37	1	146523670	146523670	+	IGR	SNP	T	T	C	rs594716	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146523670T>C								RP4-704D21.2 (48493 upstream) : RNVU1-8 (27624 downstream)																							GAAAGGATGGTCATCATCACC	0.532													.|||	74	0.0147764	0.0008	0.0591	5008	,	,		19634	0.0		0.0278	False		,,,				2504	0.0041				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGATGGTCATCAT																													1.37:g.146523670T>C			47	0	0		63	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.532										
LOC728989	728989	bcgsc.ca	37	1	146523957	146523957	+	IGR	SNP	T	T	C	rs61734778	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:146523957T>C								RP4-704D21.2 (48780 upstream) : RNVU1-8 (27337 downstream)																							CCCAACTGCATAGCACAAGAT	0.502													.|||	1743	0.348043	0.3222	0.3545	5008	,	,		19855	0.4395		0.1948	False		,,,				2504	0.4417				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACTGCATAGCACA																													1.37:g.146523957T>C			92	0	0		82	0.11	9	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	1	147313509	147313509	+	IGR	SNP	C	C	T	rs146788179	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:147313509C>T								RP11-433J22.3 (52444 upstream) : GJA8 (61436 downstream)																							GGTGGACTGTCCAAGGACAGG	0.547													C|||	36	0.0071885	0.0008	0.0072	5008	,	,		19083	0.0		0.0268	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACTGTCCAAGGA																													1.37:g.147313509C>T			188	0	0		189	0.05	9	.	0		0		RNA	SNP		37																																																																																					0	0.547										
Unknown	0	bcgsc.ca	37	1	148193730	148193730	+	IGR	SNP	G	G	A	rs61811779	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:148193730G>A								NBPF14 (167882 upstream) : PPIAL4D (8021 downstream)																							ACCCTGTCGGGAATTCCATGG	0.672													-|||	67	0.0133786	0.0	0.0187	5008	,	,		14374	0.0		0.0487	False		,,,				2504	0.0051				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTCGGGAATTCC																													1.37:g.148193730G>A			402	0	0		372	0.05	20	.	123	0.00	0		RNA	SNP		37																																																																																					0	0.672										
HRNR	388697	bcgsc.ca;mdanderson.org	37	1	152188319	152188319	+	Missense_Mutation	SNP	C	C	T	rs201547528		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:152188319C>T	ENST00000368801.2	-	3	5861	c.5786G>A	c.(5785-5787)gGc>gAc	p.G1929D	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1929					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGACGGGAGCCAGACCCATG	0.577																																					p.G1929D													.	HRNR	403		0			c.G5786A												246.0	370.0	329.0					1																	152188319		2123	4281	6404	SO:0001583	missense	388697	exon3			CGGGAGCCAGACC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5786G>A	1.37:g.152188319C>T	ENSP00000357791:p.Gly1929Asp		164	0.006097561	1		237	0.05	13	NM_001009931	0		0	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	7.393	0.631191	0.14322	.	.	ENSG00000197915	ENST00000368801	T	0.04706	3.57	3.8	0.738	0.18319	.	.	.	.	.	T	0.02304	0.0071	L	0.59436	1.845	0.09310	N	1	D	0.59357	0.985	P	0.49477	0.612	T	0.36841	-0.9731	9	0.11182	T	0.66	.	7.319	0.26517	0.0:0.5813:0.3222:0.0965	.	1929	Q86YZ3	HORN_HUMAN	D	1929	ENSP00000357791:G1929D	ENSP00000357791:G1929D	G	-	2	0	HRNR	150454943	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.344000	0.19962	0.057000	0.16193	-0.265000	0.10407	GGC			0.577	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000034016.1		XM_373868	
Unknown	0	bcgsc.ca	37	1	157029197	157029197	+	IGR	SNP	C	C	G	rs62640951	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:157029197C>G								ARHGEF11 (14035 upstream) : ETV3L (32638 downstream)																							CACAGTAGATCCATTCACCAC	0.483													C|||	94	0.01877	0.0666	0.0086	5008	,	,		19473	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTAGATCCATTCA																													1.37:g.157029197C>G			168	0	0		134	0.04	5	.	33	0.00	0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	1	157030280	157030280	+	IGR	SNP	T	T	C	rs1706	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:157030280T>C								ARHGEF11 (15118 upstream) : ETV3L (31555 downstream)																							CAATAGTGACTTGGCAGCACC	0.418													C|||	337	0.0672923	0.1203	0.0375	5008	,	,		22427	0.002		0.0885	False		,,,				2504	0.0624				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTGACTTGGCAG																													1.37:g.157030280T>C			171	0	0		170	0.05	8	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.418										
PRRX1	5396	hgsc.bcm.edu;bcgsc.ca	37	1	170695392	170695392	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:170695392G>A	ENST00000239461.6	+	3	762	c.449G>A	c.(448-450)cGc>cAc	p.R150H	PRRX1_ENST00000476867.2_3'UTR|PRRX1_ENST00000497230.2_Missense_Mutation_p.R150H|PRRX1_ENST00000367760.3_Missense_Mutation_p.R150H	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	150					artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCCAAGTTCCGCAGGAATGAG	0.498																																					p.R150H													PRRX1,colon,carcinoma,+1,1	PRRX1	1	1	0			c.G449A												67.0	62.0	64.0					1																	170695392		2203	4300	6503	SO:0001583	missense	5396	exon3			AGTTCCGCAGGAA	M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132		"""Homeoboxes / PRD class"""	9142	protein-coding gene	gene with protein product		167420	"""paired mesoderm homeo box 1"""	PMX1		1509260	Standard	NM_006902		Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.449G>A	1.37:g.170695392G>A	ENSP00000239461:p.Arg150His		209	0.009569378	2		194	0.04	8	NM_006902	34	0.00	0	B5BUM7|O60807	Missense_Mutation	SNP	ENST00000239461.6	37	CCDS1290.1	.	.	.	.	.	.	.	.	.	.	G	32	5.148692	0.94603	.	.	ENSG00000116132	ENST00000367760;ENST00000239461;ENST00000497230	D;D;D	0.97642	-4.47;-4.47;-4.47	5.63	5.63	0.86233	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.104378	0.64402	D	0.000002	D	0.99324	0.9763	H	0.99444	4.57	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.984	D	0.98552	1.0637	10	0.87932	D	0	.	18.2616	0.90038	0.0:0.0:1.0:0.0	.	150;150	P54821;P54821-2	PRRX1_HUMAN;.	H	150	ENSP00000356734:R150H;ENSP00000239461:R150H;ENSP00000450762:R150H	ENSP00000239461:R150H	R	+	2	0	PRRX1	168962016	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.168000	0.94781	2.649000	0.89929	0.650000	0.86243	CGC			0.498	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000085236.3		NM_006902	
PPFIA4	8497	bcgsc.ca	37	1	203015507	203015507	+	Silent	SNP	C	C	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:203015507C>A	ENST00000447715.2	+	13	1578	c.1137C>A	c.(1135-1137)acC>acA	p.T379T	PPFIA4_ENST00000414050.2_Silent_p.T86T|PPFIA4_ENST00000367240.2_Silent_p.T379T|PPFIA4_ENST00000295706.4_5'UTR			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	379					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CAGCCCTCACCAAGGCAAGTG	0.657																																					.													.	.			0			.												11.0	10.0	11.0					1																	203015507		874	1988	2862	SO:0001819	synonymous_variant	8497	.			CCTCACCAAGGCA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.1137C>A	1.37:g.203015507C>A			190	0	0		160	0.04	7	.	1	0.00	0	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																						0.657	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000462949.1		NM_015053	
Unknown	0	bcgsc.ca	37	1	220490435	220490435	+	IGR	SNP	T	T	C	rs7553951	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:220490435T>C								RAB3GAP2 (44639 upstream) : RP11-302I18.3 (42637 downstream)																							GTGGCTTCGCTGGCTCCCACT	0.517													T|||	1139	0.227436	0.3457	0.1729	5008	,	,		20786	0.2758		0.1243	False		,,,				2504	0.1626				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTCGCTGGCTCC																													1.37:g.220490435T>C			44	0	0		44	0.11	5	.	50	0.00	0		RNA	SNP		37																																																																																					0	0.517										
ISCA1P2	100288517	bcgsc.ca	37	1	229178058	229178058	+	IGR	SNP	C	C	T	rs4654640	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:229178058C>T								RHOU (295642 upstream) : RP5-1065P14.2 (50503 downstream)																							CAAGATAAAACAACTTCTTAA	0.408													C|||	1962	0.391773	0.3427	0.4625	5008	,	,		17416	0.2718		0.4642	False		,,,				2504	0.4571				.													.	.			0			.																																									SO:0001628	intergenic_variant	100288517	.			ATAAAACAACTTC																													1.37:g.229178058C>T			69	0.0144927536	1		65	0.14	9	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.408										
MAP1LC3C	440738	bcgsc.ca	37	1	242156734	242156734	+	IGR	SNP	C	C	T	rs28613024	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:242156734C>T	ENST00000357246.3	-	0	1182					NM_001004343.2	NP_001004343.1	Q9BXW4	MLP3C_HUMAN	microtubule-associated protein 1 light chain 3 gamma						autophagy (GO:0006914)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|microtubule (GO:0005874)|organelle membrane (GO:0031090)				endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CCACTGTGCCCTCTACGACAC	0.527													c|||	2601	0.519369	0.5772	0.4568	5008	,	,		19743	0.4494		0.501	False		,,,				2504	0.5767				.													.	.			0			.																																									SO:0001628	intergenic_variant	645980	.			TGTGCCCTCTACG	AF276659	CCDS31074.1	1q43	2014-02-12			ENSG00000197769	ENSG00000197769			13353	protein-coding gene	gene with protein product		609605				12740394	Standard	NM_001004343		Approved	ATG8J	uc001hzk.2	Q9BXW4	OTTHUMG00000039865		1.37:g.242156734C>T			32	0	0		32	0.25	8	.	0		0	A0PJY8|A2RUP0	RNA	SNP	ENST00000357246.3	37	CCDS31074.1																																																																																					0.527	MAP1LC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000096185.1		NM_001004343	
OR14A2	388761	bcgsc.ca	37	1	247886493	247886493	+	Missense_Mutation	SNP	G	G	A	rs62619787	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:247886493G>A	ENST00000366485.1	-	1	852	c.853C>T	c.(853-855)Cct>Tct	p.P285S	RP11-634B7.4_ENST00000449298.1_RNA|RP11-634B7.5_ENST00000426444.1_RNA			Q96R54	O14A2_HUMAN	olfactory receptor, family 14, subfamily A, member 2	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										TAGGTTACAGGGTTAAATACT	0.403													G|||	228	0.0455272	0.0726	0.0403	5008	,	,		16022	0.001		0.0437	False		,,,				2504	0.0603				.													.	.			0			.																																									SO:0001583	missense	388761	.			TTACAGGGTTAAA	AB065620		1q44	2013-01-16	2008-04-02	2008-04-02	ENSG00000241128	ENSG00000241128		"""GPCR / Class A : Olfactory receptors"""	15024	other	unknown			"""olfactory receptor, family 5, subfamily AX, member 1 pseudogene"", ""olfactory receptor, family 5, subfamily AX, member 1"""	OR5AX1P, OR5AX1			Standard	NG_002409		Approved			Q96R54	OTTHUMG00000040207	ENST00000366485.1:c.853C>T	1.37:g.247886493G>A	ENSP00000355441:p.Pro285Ser		238	0	0		215	0.06	12	.	0		0		Missense_Mutation	SNP	ENST00000366485.1	37		91	0.041666666666666664	42	0.08536585365853659	14	0.03867403314917127	1	0.0017482517482517483	34	0.044854881266490766	G	15.49	2.848513	0.51164	.	.	ENSG00000241128	ENST00000366485	T	0.63417	-0.04	3.0	2.05	0.26809	.	0.000000	0.44688	U	0.000429	T	0.06735	0.0172	.	.	.	0.32688	N	0.514599	.	.	.	.	.	.	T	0.55503	-0.8131	7	0.87932	D	0	.	10.1824	0.42977	0.0:0.0:0.799:0.201	rs62619787	.	.	.	S	285	ENSP00000355441:P285S	ENSP00000355441:P285S	P	-	1	0	OR14A2	245953116	1.000000	0.71417	0.004000	0.12327	0.037000	0.13140	7.252000	0.78309	0.565000	0.29255	-0.175000	0.13238	CCT			0.403	OR14A2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000096864.1		NG_002409	
OR14A2	388761	bcgsc.ca;mdanderson.org	37	1	247886615	247886615	+	Missense_Mutation	SNP	G	G	A	rs11809582	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:247886615G>A	ENST00000366485.1	-	1	730	c.731C>T	c.(730-732)aCt>aTt	p.T244I	RP11-634B7.4_ENST00000449298.1_RNA|RP11-634B7.5_ENST00000426444.1_RNA			Q96R54	O14A2_HUMAN	olfactory receptor, family 14, subfamily A, member 2	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										AGTGAAAACAGTGAGATGGGG	0.378													A|||	571	0.114018	0.3169	0.0706	5008	,	,		20509	0.001		0.0437	False		,,,				2504	0.0593				.													.	.			0			.																																									SO:0001583	missense	388761	.			AAAACAGTGAGAT	AB065620		1q44	2013-01-16	2008-04-02	2008-04-02	ENSG00000241128	ENSG00000241128		"""GPCR / Class A : Olfactory receptors"""	15024	other	unknown			"""olfactory receptor, family 5, subfamily AX, member 1 pseudogene"", ""olfactory receptor, family 5, subfamily AX, member 1"""	OR5AX1P, OR5AX1			Standard	NG_002409		Approved			Q96R54	OTTHUMG00000040207	ENST00000366485.1:c.731C>T	1.37:g.247886615G>A	ENSP00000355441:p.Thr244Ile		136	0	0		95	0.12	11	.	0		0		Missense_Mutation	SNP	ENST00000366485.1	37		206	0.09432234432234432	149	0.30284552845528456	22	0.06077348066298342	1	0.0017482517482517483	34	0.044854881266490766	A	0.004	-2.335196	0.00224	.	.	ENSG00000241128	ENST00000366485	T	0.36157	1.27	3.0	0.333	0.15943	.	0.986845	0.08224	N	0.978720	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39820	-0.9595	6	0.07990	T	0.79	.	8.9173	0.35590	0.4067:0.0:0.5933:0.0	rs11809582;rs52818459;rs58573182;rs11809582	.	.	.	I	244	ENSP00000355441:T244I	ENSP00000355441:T244I	T	-	2	0	OR14A2	245953238	0.000000	0.05858	0.000000	0.03702	0.589000	0.36550	-0.788000	0.04614	-0.372000	0.07992	-0.269000	0.10298	ACT			0.378	OR14A2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000096864.1		NG_002409	
HSD17B7P1	148818	bcgsc.ca	37	1	247990905	247990905	+	IGR	SNP	T	T	C	rs6703747	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:247990905T>C								OR14A16 (11874 upstream) : OR11L1 (13293 downstream)																							GAACATGAAGTAAGACAGAAG	0.547													C|||	661	0.131989	0.3487	0.0807	5008	,	,		17151	0.0149		0.0388	False		,,,				2504	0.092				.													.	.			0			.																																									SO:0001628	intergenic_variant	148818	.			ATGAAGTAAGACA																													1.37:g.247990905T>C			27	0	0		35	0.11	4	.	0		0		RNA	SNP		37																																																																																					0	0.547										
HSD17B7P1	148818	bcgsc.ca	37	1	247991718	247991718	+	IGR	SNP	C	C	A	rs4925725	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:247991718C>A								OR14A16 (12687 upstream) : OR11L1 (12480 downstream)																							GAAAAATTTTCTCAAAAGTTA	0.403													A|||	1142	0.228035	0.3865	0.2378	5008	,	,		20050	0.0169		0.2316	False		,,,				2504	0.2209				.													.	.			0			.																																									SO:0001628	intergenic_variant	148818	.			AATTTTCTCAAAA																													1.37:g.247991718C>A			117	0	0		75	0.23	17	.	0		0		RNA	SNP		37																																																																																					0	0.403										
OR2T8	343172	bcgsc.ca	37	1	248084825	248084825	+	Missense_Mutation	SNP	C	C	T	rs61857492	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr1:248084825C>T	ENST00000319968.4	+	1	506	c.506C>T	c.(505-507)gCa>gTa	p.A169V		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TATTGCGGTGCACACGAGATC	0.572													C|||	2384	0.476038	0.4758	0.4827	5008	,	,		13272	0.4702		0.4642	False		,,,				2504	0.4898				p.A169V													.	OR2T8	67		0			c.C506T												57.0	42.0	47.0					1																	248084825		2197	4281	6478	SO:0001583	missense	343172	exon1			GCGGTGCACACGA		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.506C>T	1.37:g.248084825C>T	ENSP00000326225:p.Ala169Val		164	0.012195122	2		181	0.18	32	NM_001005522	0		0		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	620	0.2838827838827839	166	0.33739837398373984	100	0.27624309392265195	126	0.2202797202797203	228	0.3007915567282322	C	14.44	2.535882	0.45176	.	.	ENSG00000177462	ENST00000319968	T	0.36340	1.26	3.56	2.58	0.30949	GPCR, rhodopsin-like superfamily (1);	0.796012	0.10231	U	0.699582	T	0.00012	0.0000	L	0.53617	1.68	0.80722	P	0.0	P	0.41848	0.763	P	0.46208	0.507	T	0.32851	-0.9891	9	0.87932	D	0	.	10.2888	0.43584	0.0:0.7315:0.2685:0.0	rs61857492	169	A6NH00	OR2T8_HUMAN	V	169	ENSP00000326225:A169V	ENSP00000326225:A169V	A	+	2	0	OR2T8	246151448	0.003000	0.15002	0.000000	0.03702	0.021000	0.10359	1.840000	0.39230	0.576000	0.29452	0.404000	0.27445	GCA			0.572	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000096862.1		NM_001005522	
NIFKP1	401825	bcgsc.ca	37	10	30669367	30669367	+	IGR	SNP	G	G	A	rs2149628	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:30669367G>A								MTPAP (5997 upstream) : MAP3K8 (53498 downstream)																							AATAGCAAAGGCTATGCATTT	0.403													.|||	1948	0.388978	0.23	0.4323	5008	,	,		17898	0.7222		0.2853	False		,,,				2504	0.3364				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCAAAGGCTATGC																													10.37:g.30669367G>A			28	0	0		18	0.22	4	.	0		0		RNA	SNP		37																																																																																					0	0.403										
ASAH2C	653365	bcgsc.ca;mdanderson.org	37	10	48003992	48003992	+	Missense_Mutation	SNP	C	C	T	rs142685947|rs3739968	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:48003992C>T	ENST00000426610.2	-	17	1654	c.1655G>A	c.(1654-1656)tGt>tAt	p.C552Y				P0C7U2	ASA2C_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2C	552					sphingolipid metabolic process (GO:0006665)		ceramidase activity (GO:0017040)			lung(3)	3						GGCATCATTACACACTATCTG	0.413													C|||	1736	0.346645	0.1241	0.3112	5008	,	,		11589	0.4573		0.5149	False		,,,				2504	0.3855				.													.	.			0			.																																									SO:0001583	missense	653365	.			TCATTACACACTA			10q11.22	2013-01-14			ENSG00000072444				23457	other	unknown						17334805	Standard			Approved	bA98I6.3		P0C7U2	OTTHUMG00000018134	ENST00000426610.2:c.1655G>A	10.37:g.48003992C>T	ENSP00000399947:p.Cys552Tyr		1587	0.0018903592	3		982	0.05	52	.	3	0.00	0		Missense_Mutation	SNP	ENST00000426610.2	37		.	.	.	.	.	.	.	.	.	.	C	0.056	-1.237406	0.01493	.	.	ENSG00000072444	ENST00000420079;ENST00000426610	T	0.39592	1.07	2.8	1.6	0.23607	.	0.259065	0.36972	U	0.002315	T	0.14787	0.0357	.	.	.	0.43729	P	0.003781999999999952	.	.	.	.	.	.	T	0.34030	-0.9845	6	0.02654	T	1	.	5.5884	0.17287	0.0:0.1756:0.0:0.8244	.	.	.	.	Y	540;552	ENSP00000399947:C552Y	ENSP00000392320:C540Y	C	-	2	0	ASAH2C	47523998	0.989000	0.36119	0.995000	0.50966	0.965000	0.64279	0.695000	0.25527	0.419000	0.25927	0.398000	0.26397	TGT			0.413	ASAH2C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NG_012763	
PRKRIRP3	399774	bcgsc.ca	37	10	54172174	54172174	+	IGR	SNP	G	G	A	rs7897513	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:54172174G>A								DKK1 (94757 upstream) : RP11-346D6.6 (38459 downstream)																							TCTATCGATCGCCACAACTGC	0.388													G|||	2063	0.411941	0.5325	0.2248	5008	,	,		19427	0.628		0.2276	False		,,,				2504	0.3487				.													.	.			0			.																																									SO:0001628	intergenic_variant	399774	.			TCGATCGCCACAA																													10.37:g.54172174G>A			163	0	0		106	0.07	7	.	0		0		RNA	SNP		37																																																																																					0	0.388										
NUTM2B	729262	bcgsc.ca	37	10	81471458	81471458	+	Silent	SNP	A	A	C	rs201762104	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:81471458A>C	ENST00000429828.1	+	7	2237	c.1854A>C	c.(1852-1854)ctA>ctC	p.L618L	RP11-119F19.2_ENST00000600376.1_RNA|NUTM2B_ENST00000372321.1_Intron|NUTM2B_ENST00000448135.1_Intron|RP11-119F19.2_ENST00000596088.1_RNA|RP11-119F19.2_ENST00000601369.1_RNA	NM_001278495.1	NP_001265424.1	A6NNL0	NTM2B_HUMAN	NUT family member 2B	618																	TCCCGCAGCTAGTGGAGAAGC	0.622																																					.													.	.			0			.																																									SO:0001819	synonymous_variant	729262	.			GCAGCTAGTGGAG		CCDS60574.1	10q22.3	2014-08-13	2013-03-14	2013-03-14	ENSG00000188199	ENSG00000188199			23445	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member B"""	FAM22B			Standard	NM_001278495		Approved	bA119F19.1		A6NNL0	OTTHUMG00000018572	ENST00000429828.1:c.1854A>C	10.37:g.81471458A>C			284	0	0		218	0.04	8	.	7	0.00	0	A6NM73	Silent	SNP	ENST00000429828.1	37																																																																																						0.622	NUTM2B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NG_012780	
PGGT1BP2	100132402	bcgsc.ca	37	10	81651906	81651906	+	IGR	SNP	A	A	G	rs1972481	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:81651906A>G								NUTM2E (41274 upstream) : MBL1P (28027 downstream)																							AAAGTCAGTCATGTAGAGATA	0.393													A|||	1352	0.269968	0.0651	0.2176	5008	,	,		19265	0.4683		0.2813	False		,,,				2504	0.3681				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCAGTCATGTAGA																													10.37:g.81651906A>G			111	0	0		65	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.393										
C1DP2	642538	bcgsc.ca	37	10	81791970	81791970	+	IGR	SNP	T	T	C	rs10887394	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:81791970T>C								RP11-479O17.10 (59001 upstream) : TMEM254-AS1 (14645 downstream)																							TTAATGTGTATGCAGAAACCA	0.378													.|||	875	0.17472	0.0749	0.0778	5008	,	,		23218	0.3948		0.0964	False		,,,				2504	0.2321				.													.	.			0			.																																									SO:0001628	intergenic_variant	642538	.			TGTGTATGCAGAA																													10.37:g.81791970T>C			230	0	0		171	0.08	13	.	0		0		RNA	SNP		37																																																																																					0	0.378										
Unknown	0	bcgsc.ca	37	10	120632048	120632048	+	IGR	SNP	A	A	G	rs9787461	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr10:120632048A>G								U3 (86573 upstream) : RP11-498J9.2 (130999 downstream)																							AAGTGAACACAAAGATTGGAA	0.413													N|||	2657	0.530551	0.4463	0.5836	5008	,	,		19248	0.5833		0.5378	False		,,,				2504	0.545				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAACACAAAGATT																													10.37:g.120632048A>G			78	0	0		40	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.413										
MUC2	4583	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	1090890	1090890	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:1090890C>T	ENST00000441003.2	+	28	3812	c.3785C>T	c.(3784-3786)cCg>cTg	p.P1262L	MUC2_ENST00000361558.6_5'Flank|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.P1263L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1262					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACGACACGCCCGTCCACCCTG	0.607																																					p.P1262L													.	.			0			c.C3785T												134.0	140.0	138.0					11																	1090890		2094	4199	6293	SO:0001583	missense	4583	exon28			CACGCCCGTCCAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3785C>T	11.37:g.1090890C>T	ENSP00000415183:p.Pro1262Leu		134	0	0		130	0.12	16	NM_002457	0		0	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.774	-0.046994	0.07407	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14022	2.56;2.54	3.03	1.07	0.20283	.	263.312000	0.00424	U	0.000077	T	0.15696	0.0378	L	0.59436	1.845	0.09310	N	1	B	0.17465	0.022	B	0.12837	0.008	T	0.25363	-1.0134	10	0.23891	T	0.37	.	5.5343	0.17003	0.0:0.7277:0.0:0.2723	.	1262	E7EUV1	.	L	1262;1263	ENSP00000415183:P1262L;ENSP00000351956:P1263L	ENSP00000351956:P1263L	P	+	2	0	MUC2	1080890	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.448000	0.21726	0.154000	0.19237	0.465000	0.42564	CCG			0.607	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000345894.2		NM_002457	
MUC5AC	4586	bcgsc.ca	37	11	1156646	1156646	+	Missense_Mutation	SNP	C	C	G	rs35783651	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:1156646C>G	ENST00000356191.2	+	10	655	c.655C>G	c.(655-657)Cga>Gga	p.R219G				P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	220	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		CCGTGGTCAGCGAGCTCCTCT	0.607													C|||	518	0.103435	0.1437	0.0965	5008	,	,		18368	0.003		0.1998	False		,,,				2504	0.0583				.													ENSG00000196292,NS,carcinoma,0,2	.		2	0			.							C	ARG/SER	271,1479		24,223,628	104.0	100.0	101.0		1320	0.1	0.5	11	dbSNP_126	101	826,3154		82,662,1246	no	missense	MUC5AC	XM_003403450.1	110	106,885,1874	GG,GC,CC		20.7538,15.4857,19.1449	possibly-damaging	440/1963	1156646	1097,4633	875	1990	2865	SO:0001583	missense	4586	.			GGTCAGCGAGCTC	AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182		"""Mucins"""	7515	protein-coding gene	gene with protein product		158373	"""mucin 5, subtypes A and C, tracheobronchial/gastric"""			7826332, 9588204	Standard	XM_006709945		Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000356191.2:c.655C>G	11.37:g.1156646C>G	ENSP00000348519:p.Arg219Gly		169	0	0		187	0.04	8	.	0		0	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	Missense_Mutation	SNP	ENST00000356191.2	37		263|263	0.12042124542124542|0.12042124542124542	68|68	0.13821138211382114|0.13821138211382114	42|42	0.11602209944751381|0.11602209944751381	2|2	0.0034965034965034965|0.0034965034965034965	151|151	0.19920844327176782|0.19920844327176782	c|c	0.488|0.488	-0.876505|-0.876505	0.02550|0.02550	0.154857|0.154857	0.207538|0.207538	ENSG00000215182|ENSG00000215182	ENST00000356191|ENST00000534821	T|T	0.23147|0.18174	1.92|2.23	3.28|3.28	0.102|0.102	0.14522|0.14522	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.50333|0.50333	1.59|1.59	.|.	.|.	.|.	.|P	.|0.44380	.|0.834	.|P	.|0.46452	.|0.517	T|T	0.24977|0.24977	-1.0145|-1.0145	6|8	0.30854|0.62326	T|D	0.27|0.03	.|.	8.8053|8.8053	0.34934|0.34934	0.0:0.4701:0.0:0.5299|0.0:0.4701:0.0:0.5299	rs35783651|rs35783651	.|221	.|A7Y9J9	.|.	G|R	219|221	ENSP00000348519:R219G|ENSP00000435591:S221R	ENSP00000348519:R219G|ENSP00000435591:S221R	R|S	+|+	1|3	2|2	MUC5AC|MUC5AC	1146646|1146646	0.932000|0.932000	0.31603|0.31603	0.527000|0.527000	0.27925|0.27925	0.203000|0.203000	0.24098|0.24098	0.850000|0.850000	0.27737|0.27737	-0.070000|-0.070000	0.12908|0.12908	0.443000|0.443000	0.29094|0.29094	CGA|AGC			0.607	MUC5AC-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				XM_001130382	
OR52K3P	390035	bcgsc.ca	37	11	4496613	4496613	+	IGR	SNP	C	C	A	rs9633905	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:4496613C>A								OR52K2 (25022 upstream) : OR52K1 (13495 downstream)																							GCTGTGGGAACACTAGCTTCA	0.483													C|||	1271	0.253794	0.115	0.2896	5008	,	,		23441	0.371		0.3121	False		,,,				2504	0.2352				.													.	.			0			.																																									SO:0001628	intergenic_variant	390035	.			TGGGAACACTAGC																													11.37:g.4496613C>A			111	0	0		107	0.06	6	.	0		0		RNA	SNP		37																																																																																					0	0.483										
OTOG	340990	bcgsc.ca;mdanderson.org	37	11	17631751	17631751	+	Missense_Mutation	SNP	C	C	T	rs2041028	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:17631751C>T	ENST00000399391.2	+	35	4940	c.4940C>T	c.(4939-4941)cCa>cTa	p.P1647L	OTOG_ENST00000342528.2_Missense_Mutation_p.P653L|OTOG_ENST00000399397.1_Missense_Mutation_p.P1574L	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	1647	Pro-rich.				adult locomotory behavior (GO:0008344)|L-arabinose metabolic process (GO:0046373)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	alpha-L-arabinofuranosidase activity (GO:0046556)|structural molecule activity (GO:0005198)			breast(3)|central_nervous_system(1)|lung(1)|skin(1)	6						ACGACACCCCCACAGCCCTCC	0.652													T|||	2177	0.434704	0.649	0.2695	5008	,	,		16761	0.2222		0.3767	False		,,,				2504	0.5409				.													.	.			0			.																																									SO:0001583	missense	340990	.			CACCCCCACAGCC	AK128214	CCDS59225.1	11p14.3	2014-07-17			ENSG00000188162	ENSG00000188162			8516	protein-coding gene	gene with protein product		604487				9405633	Standard	NM_001277269		Approved	mlemp, OTGN, FLJ46346	uc031pzc.1	Q6ZRI0	OTTHUMG00000149905	ENST00000399391.2:c.4940C>T	11.37:g.17631751C>T	ENSP00000382323:p.Pro1647Leu		109	0	0		88	0.08	7	.	1	0.00	0	A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	ENST00000399391.2	37	CCDS59225.1	791	0.36217948717948717	307	0.6239837398373984	98	0.27071823204419887	95	0.1660839160839161	291	0.3839050131926121	T	5.784	0.328982	0.10956	.	.	ENSG00000188162	ENST00000399391;ENST00000399397;ENST00000342528	T;T;T	0.14640	2.49;2.61;2.93	5.25	4.13	0.48395	.	0.108148	0.36703	N	0.002460	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37361	-0.9709	9	0.06625	T	0.88	.	6.2849	0.21027	0.0:0.1928:0.0:0.8072	rs2041028;rs61262367;rs2041028	653	Q6ZRI0-2	.	L	1647;1574;653	ENSP00000382323:P1647L;ENSP00000382329:P1574L;ENSP00000341666:P653L	ENSP00000341666:P653L	P	+	2	0	OTOG	17588327	0.000000	0.05858	0.024000	0.17045	0.095000	0.18619	0.105000	0.15333	0.841000	0.35020	-0.254000	0.11334	CCA			0.652	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
OTOG	340990	ucsc.edu;bcgsc.ca;mdanderson.org	37	11	17632651	17632651	+	Missense_Mutation	SNP	C	C	T	rs7111528	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:17632651C>T	ENST00000399391.2	+	35	5840	c.5840C>T	c.(5839-5841)aCg>aTg	p.T1947M	OTOG_ENST00000342528.2_Missense_Mutation_p.T953M|OTOG_ENST00000399397.1_Missense_Mutation_p.T1874M	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	1947			T -> M (in dbSNP:rs7111528).		adult locomotory behavior (GO:0008344)|L-arabinose metabolic process (GO:0046373)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	alpha-L-arabinofuranosidase activity (GO:0046556)|structural molecule activity (GO:0005198)			breast(3)|central_nervous_system(1)|lung(1)|skin(1)	6						ACAGAGCTCACGCCTGCTACG	0.627													T|||	2019	0.403155	0.5325	0.2637	5008	,	,		20540	0.2222		0.3767	False		,,,				2504	0.5409				.													.	.			0			.																																									SO:0001583	missense	340990	.			AGCTCACGCCTGC	AK128214	CCDS59225.1	11p14.3	2014-07-17			ENSG00000188162	ENSG00000188162			8516	protein-coding gene	gene with protein product		604487				9405633	Standard	NM_001277269		Approved	mlemp, OTGN, FLJ46346	uc031pzc.1	Q6ZRI0	OTTHUMG00000149905	ENST00000399391.2:c.5840C>T	11.37:g.17632651C>T	ENSP00000382323:p.Thr1947Met		91	0	0		88	0.10	9	.	0		0	A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	ENST00000399391.2	37	CCDS59225.1	745	0.3411172161172161	264	0.5365853658536586	95	0.26243093922651933	95	0.1660839160839161	291	0.3839050131926121	T	5.834	0.338036	0.11013	.	.	ENSG00000188162	ENST00000399391;ENST00000399397;ENST00000342528	T;T;T	0.18810	2.19;2.32;2.62	4.29	-0.815	0.10843	.	1.238560	0.05384	N	0.537759	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.47636	-0.9102	9	0.40728	T	0.16	.	9.178	0.37123	0.0:0.5385:0.0:0.4615	rs7111528;rs7111528	953	Q6ZRI0-2	.	M	1947;1874;953	ENSP00000382323:T1947M;ENSP00000382329:T1874M;ENSP00000341666:T953M	ENSP00000341666:T953M	T	+	2	0	OTOG	17589227	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.697000	0.05098	-0.371000	0.08004	-1.361000	0.01213	ACG			0.627	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
DGKZ	8525	broad.mit.edu	37	11	46393272	46393274	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AAG	AAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:46393272_46393274delAAG	ENST00000454345.1	+	10	1467_1469	c.1342_1344delAAG	c.(1342-1344)aagdel	p.K451del	DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000318201.8_In_Frame_Del_p.K240del|DGKZ_ENST00000532868.2_In_Frame_Del_p.K267del|DGKZ_ENST00000421244.2_In_Frame_Del_p.K263del|DGKZ_ENST00000456247.2_In_Frame_Del_p.K262del|DGKZ_ENST00000527911.1_In_Frame_Del_p.K263del|DGKZ_ENST00000343674.6_In_Frame_Del_p.K279del|DGKZ_ENST00000395574.3_In_Frame_Del_p.K229del|DGKZ_ENST00000528615.1_In_Frame_Del_p.K41del	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	451	MARCKS homology.|Poly-Lys.				blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GAAAGCAAGCAAGAAGAAGAAGA	0.601																																					p.448_448del													.	DGKZ	199		0			c.1342_1344del																																									SO:0001651	inframe_deletion	8525	exon10			GCAAGCAAGAAGA	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.1342_1344delAAG	11.37:g.46393281_46393283delAAG	ENSP00000412178:p.Lys451del		195	0	0		167	0.04	7	NM_001105540	48	0.00	0	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	In_Frame_Del	DEL	ENST00000454345.1	37	CCDS41640.1																																																																																					0.601	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000389772.1		NM_001105540	
LOC440040	440040	broad.mit.edu;ucsc.edu	37	11	49831483	49831483	+	RNA	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:49831483C>T	ENST00000527477.1	+	0	1708																											GTGGGGGACTCTTGGAATTGG	0.458																																					.													.	.			0			.																																											0	.			GGGACTCTTGGAA																													11.37:g.49831483C>T			133	0	0		114	0.22	25	.	4	0.25	1		RNA	SNP	ENST00000527477.1	37																																																																																						0.458	RP11-707M1.1-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000391378.2			
OR4C50P	256190	bcgsc.ca	37	11	51527482	51527482	+	IGR	SNP	C	C	T	rs35049610	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:51527482C>T								OR4C46 (11271 upstream) : None (None downstream)																							ATCTCAGTAGCACCAAAAATG	0.463													.|||	398	0.0794728	0.0492	0.0591	5008	,	,		21327	0.0863		0.1252	False		,,,				2504	0.0808				.													.	.			0			.																																									SO:0001628	intergenic_variant	256190	.			CAGTAGCACCAAA																													11.37:g.51527482C>T			62	0	0		57	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.463										
EEF1DP8	283236	bcgsc.ca	37	11	61936839	61936839	+	IGR	SNP	G	G	C	rs17156910	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:61936839G>C								INCENP (16204 upstream) : SCGB1D1 (20848 downstream)																							AAAGGAGATTGTACGAGCAAA	0.488													C|||	644	0.128594	0.348	0.1715	5008	,	,		18442	0.0139		0.008	False		,,,				2504	0.044				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGATTGTACGAG																													11.37:g.61936839G>C			40	0	0		41	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.488										
UBTFL2	120126	bcgsc.ca	37	11	89486848	89486848	+	lincRNA	SNP	C	C	G	rs11018769	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:89486848C>G	ENST00000527332.1	-	0	972																											AAAGTCTGGACAGTTCCTGTA	0.413																																					.													.	.			0			.							C		122,3492		0,122,1685	90.0	103.0	99.0			-3.3	0.0	11	dbSNP_120	99	943,7217		0,943,3137	no	intergenic				0,1065,4822	GG,GC,CC		11.5564,3.3758,9.0454			89486848	1065,10709	1807	4080	5887			120126	.			TCTGGACAGTTCC																													11.37:g.89486848C>G			234	0	0		245	0.04	11	.	0		0		RNA	SNP	ENST00000527332.1	37																																																																																						0.413	RP11-313I2.11-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000395428.1			
OR10G5P	79515	bcgsc.ca	37	11	123880482	123880482	+	IGR	SNP	T	T	G	rs11601573	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:123880482T>G								OR10G6 (14614 upstream) : OR10G4 (5799 downstream)																							GGGAACCTCCTCATCCTGCTG	0.527													T|||	1028	0.205272	0.3192	0.1513	5008	,	,		20917	0.1002		0.2137	False		,,,				2504	0.1892				.													.	.			0			.																																									SO:0001628	intergenic_variant	79515	.			ACCTCCTCATCCT																													11.37:g.123880482T>G			147	0	0		127	0.04	5	.	0		0		RNA	SNP		37																																																																																					0	0.527										
OR10G5P	79515	bcgsc.ca	37	11	123880685	123880685	+	IGR	SNP	G	G	A	rs55700020	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:123880685G>A								OR10G6 (14817 upstream) : OR10G4 (5596 downstream)																							GGGGAGCACCGAGTGTTTGCT	0.502													G|||	1052	0.210064	0.3366	0.1527	5008	,	,		19214	0.1002		0.2137	False		,,,				2504	0.1892				.													.	.			0			.																																									SO:0001628	intergenic_variant	79515	.			AGCACCGAGTGTT																													11.37:g.123880685G>A			129	0	0		99	0.07	7	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	11	133734907	133734907	+	IGR	SNP	T	T	G	rs10894754	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr11:133734907T>G								SPATA19 (19474 upstream) : MIR4697 (33491 downstream)																							CCGGGAGCCGTCGTGCCCACC	0.602													T|||	690	0.13778	0.1747	0.2435	5008	,	,		16853	0.1032		0.1362	False		,,,				2504	0.0501				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGCCGTCGTGCC																													11.37:g.133734907T>G			47	0	0		42	0.12	5	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.602										
WNK1	65125	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	994115	994115	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:994115G>A	ENST00000315939.6	+	19	4788	c.4145G>A	c.(4144-4146)gGg>gAg	p.G1382E	WNK1_ENST00000535572.1_Missense_Mutation_p.G1135E|WNK1_ENST00000537687.1_Missense_Mutation_p.G1642E|WNK1_ENST00000530271.2_Missense_Mutation_p.G1880E|WNK1_ENST00000340908.4_Missense_Mutation_p.G975E	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1382					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ACTGAAGAGGGGATTGCTGGA	0.517																																					p.G1642E	Colon(19;451 567 6672 12618 28860)												.	.			0			c.G4925A												121.0	117.0	118.0					12																	994115		2203	4300	6503	SO:0001583	missense	65125	exon19			AAGAGGGGATTGC	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.4145G>A	12.37:g.994115G>A	ENSP00000313059:p.Gly1382Glu		187	0	0		264	0.11	28	NM_001184985	117	0.06	7	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	3.482	-0.105738	0.06924	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.15	3.17	0.36434	.	0.296573	0.29165	N	0.012952	T	0.29817	0.0745	L	0.43152	1.355	0.09310	N	1	P;P;P	0.47762	0.835;0.9;0.845	P;P;B	0.49999	0.453;0.628;0.33	T	0.09357	-1.0678	10	0.52906	T	0.07	-5.2924	4.1749	0.10348	0.079:0.2544:0.4567:0.21	.	1135;1135;1382	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	E	1135;1382;1642;555;1880;975	ENSP00000441972:G1135E;ENSP00000313059:G1382E;ENSP00000444465:G1642E;ENSP00000433548:G1880E;ENSP00000341292:G975E	ENSP00000252477:G555E	G	+	2	0	WNK1	864376	0.952000	0.32445	0.070000	0.20053	0.123000	0.20343	0.744000	0.26245	1.273000	0.44346	-0.176000	0.13171	GGG			0.517	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206683.1		NM_018979	
Unknown	0	bcgsc.ca	37	12	6588445	6588445	+	IGR	SNP	A	A	G	rs2008134	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:6588445A>G								VAMP1 (8292 upstream) : MRPL51 (12704 downstream)																							GCTGGCCCTGATAGGAGAAAA	0.483													A|||	1101	0.219848	0.0204	0.1859	5008	,	,		19439	0.3304		0.329	False		,,,				2504	0.2873				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCCCTGATAGGAG																													12.37:g.6588445A>G			60	0	0		108	0.07	8	.	0		0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	12	8786982	8786982	+	IGR	SNP	T	T	C	rs12308718	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:8786982T>C								AICDA (21515 upstream) : MFAP5 (11569 downstream)																							TACCGGGCGATTGGCATCCTC	0.512													T|||	120	0.0239617	0.0862	0.0086	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGCGATTGGCAT																													12.37:g.8786982T>C			86	0	0		106	0.08	8	.	0		0		RNA	SNP		37																																																																																					0	0.512										
GABARAPL1	23710	bcgsc.ca	37	12	10370734	10370734	+	Missense_Mutation	SNP	C	C	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:10370734C>G	ENST00000266458.5	+	2	488	c.163C>G	c.(163-165)Ctt>Gtt	p.L55V	GABARAPL1_ENST00000535576.1_5'UTR|GABARAPL1_ENST00000539170.1_5'UTR|GABARAPL1_ENST00000543602.1_Missense_Mutation_p.L55V|GABARAPL1_ENST00000544284.1_5'UTR|GABARAPL1_ENST00000546017.1_5'UTR|GABARAPL1_ENST00000539289.1_3'UTR|GABARAPL1_ENST00000545887.1_Missense_Mutation_p.L55V|GABARAPL1_ENST00000421801.2_Missense_Mutation_p.L55V|GABARAPL1_ENST00000545047.1_Intron	NM_031412.2	NP_113600.1	Q9H0R8	GBRL1_HUMAN	GABA(A) receptor-associated protein like 1	55	Interaction with GABRG2. {ECO:0000250}.				autophagy (GO:0006914)	autophagic vacuole (GO:0005776)|cell body (GO:0044297)|cytoplasmic vesicle (GO:0031410)|dendrite cytoplasm (GO:0032839)|dendrite membrane (GO:0032590)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|microtubule (GO:0005874)	beta-tubulin binding (GO:0048487)|GABA receptor binding (GO:0050811)			NS(1)|lung(1)	2						GCCCTCTGACCTTACTGGTAA	0.488																																					p.L55V	Melanoma(3;46 76 4652 22680 42285)												.	GABARAPL1	10		0			c.C163G												212.0	175.0	187.0					12																	10370734		2203	4300	6503	SO:0001583	missense	23710	exon2			TCTGACCTTACTG	AF087847	CCDS8620.1	12p13.31	2014-02-12			ENSG00000139112	ENSG00000139112			4068	protein-coding gene	gene with protein product		607420				11414770, 11374880	Standard	NM_031412		Approved	gec1, APG8L, ATG8L, ATG8B	uc001qxs.3	Q9H0R8	OTTHUMG00000168411	ENST00000266458.5:c.163C>G	12.37:g.10370734C>G	ENSP00000266458:p.Leu55Val		195	0	0		324	0.03	11	NM_031412	211	0.04	9	B4E0Y7|Q6FIE6	Missense_Mutation	SNP	ENST00000266458.5	37	CCDS8620.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.295014	0.81025	.	.	ENSG00000139112	ENST00000545859;ENST00000266458;ENST00000421801;ENST00000543602;ENST00000545887	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	4.97	4.97	0.65823	.	0.000000	0.56097	D	0.000025	T	0.68622	0.3021	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.87578	0.998;0.997	T	0.72343	-0.4322	10	0.62326	D	0.03	.	15.7294	0.77790	0.0:1.0:0.0:0.0	.	55;55	B4E0Y7;Q9H0R8	.;GBRL1_HUMAN	V	55	ENSP00000444108:L55V;ENSP00000266458:L55V;ENSP00000411256:L55V;ENSP00000445857:L55V;ENSP00000444186:L55V	ENSP00000266458:L55V	L	+	1	0	GABARAPL1	10262001	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.627000	0.67784	2.297000	0.77311	0.650000	0.86243	CTT			0.488	GABARAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000399651.1	rescued with RNA-seq		
HEBP1	50865	bcgsc.ca	37	12	13140216	13140216	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:13140216C>T	ENST00000014930.4	-	3	426	c.268G>A	c.(268-270)Gaa>Aaa	p.E90K	HEBP1_ENST00000536942.1_Missense_Mutation_p.E90K|RP11-392P7.6_ENST00000499948.2_RNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	90					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		GAGCCATCTTCATTGGGGAAC	0.468																																					p.E90K													.	HEBP1	16		0			c.G268A												83.0	83.0	83.0					12																	13140216		2203	4300	6503	SO:0001583	missense	50865	exon3			CATCTTCATTGGG	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.268G>A	12.37:g.13140216C>T	ENSP00000014930:p.Glu90Lys		150	0.0066666667	1		376	0.03	13	NM_015987	287	0.05	13	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	37	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.834769	0.50951	.	.	ENSG00000013583	ENST00000014930;ENST00000535636;ENST00000536942	T;T;T	0.21734	1.99;1.99;1.99	5.66	3.79	0.43588	Regulatory factor, effector, bacterial (1);	0.511846	0.23610	N	0.046350	T	0.25306	0.0615	M	0.71036	2.16	0.09310	N	1	B	0.27316	0.175	B	0.35470	0.203	T	0.28554	-1.0040	10	0.10111	T	0.7	-15.9027	11.7468	0.51825	0.0:0.8091:0.1238:0.0671	.	90	Q9NRV9	HEBP1_HUMAN	K	90;19;90	ENSP00000014930:E90K;ENSP00000442020:E19K;ENSP00000441678:E90K	ENSP00000014930:E90K	E	-	1	0	HEBP1	13031483	0.543000	0.26434	0.005000	0.12908	0.994000	0.84299	2.695000	0.47043	0.824000	0.34613	0.655000	0.94253	GAA			0.468	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401001.1	rescued with RNA-seq		
EEF1A1P16	387845	bcgsc.ca	37	12	17144587	17144587	+	IGR	SNP	C	C	T	rs61265963	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:17144587C>T								RP11-239A17.1 (203808 upstream) : RNU6-837P (79744 downstream)																							ACAGCAAAAACGACCCACCAA	0.493													c|||	386	0.0770767	0.028	0.1888	5008	,	,		20764	0.2054		0.0	False		,,,				2504	0.0112				.													.	.			0			.																																									SO:0001628	intergenic_variant	390352	.			CAAAAACGACCCA																													12.37:g.17144587C>T			32	0	0		62	0.08	5	.	6	0.67	4		RNA	SNP		37																																																																																					0	0.493										
RP11-405A12.2	0	bcgsc.ca	37	12	20094524	20094524	+	lincRNA	SNP	G	G	T	rs1844950	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:20094524G>T	ENST00000535764.1	+	0	212																											TGCAGCTAATGTTCTTTGTGA	0.398													G|||	1552	0.309904	0.2958	0.2968	5008	,	,		18777	0.5685		0.2247	False		,,,				2504	0.1595				.													.	.			0			.																																											0	.			GCTAATGTTCTTT																													12.37:g.20094524G>T			208	0	0		312	0.03	10	.	0		0		RNA	SNP	ENST00000535764.1	37																																																																																						0.398	RP11-405A12.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000401672.1			
ITPR2	3709	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	26811025	26811025	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:26811025G>A	ENST00000381340.3	-	17	2341	c.1925C>T	c.(1924-1926)aCc>aTc	p.T642I		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	642					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GATAGCAGTGGTATTAGACAC	0.338																																					p.T642I													.	.			0			c.C1925T												95.0	86.0	89.0					12																	26811025		1839	4091	5930	SO:0001583	missense	3709	exon17			GCAGTGGTATTAG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1925C>T	12.37:g.26811025G>A	ENSP00000370744:p.Thr642Ile		231	0	0		403	0.10	42	NM_002223	14	0.14	2	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989094	0.35131	.	.	ENSG00000123104	ENST00000381340	D	0.95342	-3.68	4.8	2.82	0.32997	Intracellular calcium-release channel (1);	0.097598	0.64402	D	0.000001	D	0.87822	0.6274	N	0.08118	0	0.80722	D	1	B	0.26602	0.154	B	0.36134	0.218	D	0.84628	0.0688	10	0.62326	D	0.03	.	9.1165	0.36762	0.0:0.147:0.5698:0.2832	.	642	Q14571	ITPR2_HUMAN	I	642	ENSP00000370744:T642I	ENSP00000370744:T642I	T	-	2	0	ITPR2	26702292	1.000000	0.71417	0.967000	0.41034	0.821000	0.46438	4.000000	0.57039	1.204000	0.43247	0.655000	0.94253	ACC			0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000402732.1		NM_002223	
ERGIC2	51290	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	29521221	29521221	+	Splice_Site	SNP	C	C	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:29521221C>A	ENST00000360150.4	-	4	291		c.e4-1			NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2						vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					TCTTAATTTGCTGAAAGACAA	0.294																																					.													.	.			0			c.216-1G>T												55.0	52.0	53.0					12																	29521221		1796	4059	5855	SO:0001630	splice_region_variant	51290	exon5			AATTTGCTGAAAG	AF216751	CCDS41765.1	12p11.22	2006-02-08							30208	protein-coding gene	gene with protein product		612236				11445006, 12932305	Standard	NM_016570		Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.216-1G>T	12.37:g.29521221C>A			422	0	0		706	0.08	54	NM_016570	12	0.00	0	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Splice_Site	SNP	ENST00000360150.4	37	CCDS41765.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559313	0.45590	.	.	ENSG00000087502	ENST00000360150;ENST00000201023;ENST00000552155;ENST00000546839;ENST00000550353;ENST00000552132	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.47	0.87643	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ERGIC2	29412488	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	7.334000	0.79224	2.733000	0.93635	0.579000	0.79373	.			0.294	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000403489.1		NM_016570	Intron
MUC19	283463	bcgsc.ca	37	12	40826514	40826514	+	Silent	SNP	T	T	C	rs10506162	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:40826514T>C	ENST00000454784.4	+	17	1777	c.1044T>C	c.(1042-1044)ccT>ccC	p.P348P	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	348	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						AAATTGTTCCTGTGATGCAAT	0.338													T|||	268	0.0535144	0.0129	0.0706	5008	,	,		16878	0.0208		0.1541	False		,,,				2504	0.0266				.													.	.			0			.																																									SO:0001819	synonymous_variant	283463	.			TGTTCCTGTGATG	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.1044T>C	12.37:g.40826514T>C			167	0.0119760479	2		143	0.11	16	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.338	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40834918	40834918	+	Missense_Mutation	SNP	C	C	T	rs4768261	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:40834918C>T	ENST00000454784.4	+	24	2658	c.1925C>T	c.(1924-1926)tCt>tTt	p.S642F	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	642			S -> F (in dbSNP:rs4768261).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						GTTCGAAATTCTAAAGGGATA	0.408													C|||	268	0.0535144	0.0257	0.072	5008	,	,		13366	0.0188		0.1451	False		,,,				2504	0.0194				.													.	.			0			.																																									SO:0001583	missense	283463	.			GAAATTCTAAAGG	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.1925C>T	12.37:g.40834918C>T	ENSP00000476404:p.Ser642Phe		207	0	0		153	0.13	20	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		177	0.08104395604395605	20	0.04065040650406504	28	0.07734806629834254	8	0.013986013986013986	121	0.15963060686015831	C	17.48	3.399749	0.62177	.	.	ENSG00000205592	ENST00000425730	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	T	0.00967	0.0032	M	0.88241	2.94	0.09310	P	0.999999999783001	.	.	.	.	.	.	T	0.40534	-0.9558	5	0.54805	T	0.06	.	13.597	0.61996	0.156:0.844:0.0:0.0	rs4768261;rs17528972;rs52816490;rs60702824;rs4768261	.	.	.	F	871	.	ENSP00000395253:S871F	S	+	2	0	MUC19	39121185	0.975000	0.34042	1.000000	0.80357	0.948000	0.59901	1.017000	0.29989	2.618000	0.88619	0.650000	0.86243	TCT			0.408	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40835749	40835749	+	Silent	SNP	T	T	C	rs11176655	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:40835749T>C	ENST00000454784.4	+	25	2830	c.2097T>C	c.(2095-2097)caT>caC	p.H699H	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	699	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						GGGAAGGTCATGTTAGAACTT	0.373													T|||	861	0.171925	0.1566	0.1412	5008	,	,		17039	0.3204		0.1024	False		,,,				2504	0.1329				.													.	.			0			.																																									SO:0001819	synonymous_variant	283463	.			AGGTCATGTTAGA	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.2097T>C	12.37:g.40835749T>C			203	0	0		189	0.04	7	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.373	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40837898	40837898	+	Missense_Mutation	SNP	G	G	A	rs11564109	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:40837898G>A	ENST00000454784.4	+	28	3213	c.2480G>A	c.(2479-2481)tGt>tAt	p.C827Y	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	827	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		C -> Y (in dbSNP:rs11564109).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						TGTGGTCTTTGTGGAAATAAC	0.373													G|||	422	0.0842652	0.1369	0.0821	5008	,	,		21755	0.0188		0.1451	False		,,,				2504	0.0194				.													.	.			0			.																																									SO:0001583	missense	283463	.			GTCTTTGTGGAAA	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.2480G>A	12.37:g.40837898G>A	ENSP00000476404:p.Cys827Tyr		93	0	0		99	0.14	14	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		245	0.11217948717948718	84	0.17073170731707318	32	0.08839779005524862	8	0.013986013986013986	121	0.15963060686015831	G	18.58	3.653932	0.67472	.	.	ENSG00000205592	ENST00000425730	.	.	.	4.33	4.33	0.51752	.	.	.	.	.	T	0.01320	0.0043	H	0.95004	3.61	0.09310	P	1.0	.	.	.	.	.	.	T	0.47724	-0.9095	5	0.87932	D	0	.	16.4538	0.84007	0.0:0.0:1.0:0.0	rs11564109;rs17445071;rs17492446;rs17529502;rs52830822;rs57686937;rs11564109	.	.	.	Y	1056	.	ENSP00000395253:C1056Y	C	+	2	0	MUC19	39124165	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	9.217000	0.95160	2.362000	0.80069	0.491000	0.48974	TGT			0.373	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40843504	40843504	+	Silent	SNP	A	A	C	rs12581232	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:40843504A>C	ENST00000454784.4	+	34	3934	c.3201A>C	c.(3199-3201)acA>acC	p.T1067T				Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	1067	Approximate repeats of G-V-T-G-T-T-G-P-S- A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						CCACTACAACAGCTACCACCA	0.299													A|||	860	0.171725	0.1558	0.1412	5008	,	,		15610	0.3204		0.1024	False		,,,				2504	0.1329				.													.	.			0			.																																									SO:0001819	synonymous_variant	283463	.			TACAACAGCTACC	AY236870		12q12	2012-04-20	2006-03-14		ENSG00000205592	ENSG00000205592		"""Mucins"""	14362	protein-coding gene	gene with protein product		612170				12882755	Standard	NM_173600		Approved	FLJ35746	uc021qxa.1	Q7Z5P9	OTTHUMG00000060732	ENST00000454784.4:c.3201A>C	12.37:g.40843504A>C			827	0.0036275695	3		683	0.04	29	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.299	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
Unknown	0	bcgsc.ca	37	12	43963769	43963769	+	IGR	SNP	A	A	G	rs75198585	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:43963769A>G								ADAMTS20 (18045 upstream) : RP11-350F4.2 (149026 downstream)																							CCGTTTTCATACTGCTCATTC	0.408													A|||	84	0.0167732	0.0023	0.0274	5008	,	,		20483	0.0		0.0477	False		,,,				2504	0.0143				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTCATACTGCTC																													12.37:g.43963769A>G			58	0	0		39	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.408										
Unknown	0	bcgsc.ca	37	12	43964280	43964281	+	IGR	DNP	GT	GT	TG	rs34593988|rs11831774|rs11833398	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:43964280_43964281GT>TG								ADAMTS20 (18556 upstream) : RP11-350F4.2 (148514 downstream)																							ACTTCGTTGAGTGAATGCAATA	0.406																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGTTGAGTGAATG																													12.37:g.43964280_43964281delinsTG			85	0	0		73	0.08	6	.	0		0		RNA	DNP		37																																																																																					0	0.406										
Unknown	0	bcgsc.ca	37	12	43965011	43965011	+	IGR	SNP	A	A	T	rs66501365	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:43965011A>T								ADAMTS20 (19287 upstream) : RP11-350F4.2 (147784 downstream)																							AACCTCACCAACACAGGTAGG	0.423													A|||	871	0.173922	0.3298	0.0893	5008	,	,		20662	0.1438		0.0915	False		,,,				2504	0.1391				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCACCAACACAGG																													12.37:g.43965011A>T			111	0	0		92	0.11	10	.	0		0		RNA	SNP		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	12	43965468	43965468	+	IGR	SNP	G	G	T	rs67397305	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:43965468G>T								ADAMTS20 (19744 upstream) : RP11-350F4.2 (147327 downstream)																							TTTTGTTCCTGCTCAGAAGTT	0.388													G|||	559	0.111621	0.2753	0.0735	5008	,	,		18387	0.0258		0.0755	False		,,,				2504	0.0429				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCCTGCTCAGA																													12.37:g.43965468G>T			74	0	0		62	0.08	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.388										
KRT86	3892	bcgsc.ca	37	12	52646139	52646139	+	Intron	SNP	G	G	A	rs146544749	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:52646139G>A	ENST00000544024.1	+	1	129				KRT121P_ENST00000529785.1_RNA			O43790	KRT86_HUMAN	keratin 86							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCCTGATCAGGCAGGCCATG	0.642													G|||	37	0.00738818	0.0	0.0187	5008	,	,		17721	0.0		0.0229	False		,,,				2504	0.001				.													.	.			0			.																																									SO:0001627	intron_variant	85349	.			TGATCAGGCAGGC	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000544024.1:c.-5+2927G>A	12.37:g.52646139G>A			130	0	0		127	0.09	11	.	2	0.00	0	P78387	RNA	SNP	ENST00000544024.1	37	CCDS41785.1																																																																																					0.642	KRT86-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_002284	
EIF4B	1975	ucsc.edu;mdanderson.org	37	12	53431298	53431298	+	Missense_Mutation	SNP	T	T	A	rs146008363	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:53431298T>A	ENST00000262056.9	+	11	1738	c.1412T>A	c.(1411-1413)cTa>cAa	p.L471Q	EIF4B_ENST00000420463.3_Missense_Mutation_p.L476Q|RP11-983P16.4_ENST00000546566.1_RNA|EIF4B_ENST00000416762.3_Missense_Mutation_p.L432Q|RP11-983P16.4_ENST00000552905.1_RNA|RP11-983P16.4_ENST00000550601.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	471				L -> Q (in Ref. 6; AAH73154). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						GATCAGCCCCTAAAGGTAATG	0.498													T|||	90	0.0179712	0.0023	0.0231	5008	,	,		21260	0.0		0.0636	False		,,,				2504	0.0072				p.L471Q													.	EIF4B	38		0			c.T1412A							T	GLN/LEU	37,3567		0,37,1765	26.0	24.0	25.0		1412	5.0	1.0	12	dbSNP_134	25	441,7651		16,409,3621	no	missense	EIF4B	NM_001417.4	113	16,446,5386	AA,AT,TT		5.4498,1.0266,4.0869	probably-damaging	471/612	53431298	478,11218	1802	4046	5848	SO:0001583	missense	1975	exon11			AGCCCCTAAAGGT	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"""RNA binding motif (RRM) containing"""	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.1412T>A	12.37:g.53431298T>A	ENSP00000262056:p.Leu471Gln		279	0	0		244	0.10	24	NM_001417	672	0.00	1	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Missense_Mutation	SNP	ENST00000262056.9	37	CCDS41788.1	62	0.028388278388278388	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	49	0.06464379947229551	T	19.71	3.877576	0.72294	0.010266	0.054498	ENSG00000063046	ENST00000262056;ENST00000420463;ENST00000430205;ENST00000416762	T;T;T	0.57595	0.39;0.39;0.39	4.96	4.96	0.65561	.	0.000000	0.64402	D	0.000001	T	0.21186	0.0510	M	0.71581	2.175	0.48135	D	0.999595	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.999;0.997;0.999;0.999	T	0.49312	-0.8953	10	0.19147	T	0.46	.	13.2256	0.59912	0.0:0.0:0.0:1.0	.	432;476;447;471	B4DS13;E7EX17;E7EPC9;P23588	.;.;.;IF4B_HUMAN	Q	471;476;447;432	ENSP00000262056:L471Q;ENSP00000388806:L476Q;ENSP00000412530:L432Q	ENSP00000262056:L471Q	L	+	2	0	EIF4B	51717565	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.589000	0.61006	2.176000	0.68965	0.477000	0.44152	CTA			0.498	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000404852.2		NM_001417	
PHC1P1	653441	bcgsc.ca	37	12	55805647	55805647	+	IGR	SNP	A	A	G	rs12825123	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:55805647A>G								OR6C65 (10358 upstream) : OR6C76 (14390 downstream)																							ATTCCTCTGCAATCTCTTGGC	0.483													-|||	1063	0.21226	0.18	0.2435	5008	,	,		19674	0.1071		0.2465	False		,,,				2504	0.3067				.													.	.			0			.																																									SO:0001628	intergenic_variant	653441	.			CTCTGCAATCTCT																													12.37:g.55805647A>G			405	0	0		333	0.06	20	.	394	0.00	0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	12	75057687	75057687	+	IGR	SNP	G	G	A	rs7311420	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:75057687G>A								ATXN7L3B (122464 upstream) : RP11-81K13.1 (357061 downstream)																							ACCAACAGGAGGAAGGCTTGA	0.453													A|||	2635	0.526158	0.8351	0.4352	5008	,	,		19378	0.3651		0.3897	False		,,,				2504	0.4796				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACAGGAGGAAGGC																													12.37:g.75057687G>A			53	0	0		45	0.09	4	.	0		0		RNA	SNP		37																																																																																					0	0.453										
CFAP54	144535	bcgsc.ca	37	12	97098549	97098549	+	Missense_Mutation	SNP	T	T	C	rs11108643	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:97098549T>C	ENST00000524981.4	+	47	6526	c.6503T>C	c.(6502-6504)cTt>cCt	p.L2168P				Q96N23	CL055_HUMAN		0																	TCAGGAAAACTTCTTACCAGT	0.264													C|||	4110	0.820687	0.9705	0.8386	5008	,	,		10727	0.9077		0.7286	False		,,,				2504	0.6104				.													.	.			0			.							C		4010,346		1854,302,22	34.0	37.0	36.0			4.9	1.0	12	dbSNP_120	36	5904,2594		2065,1774,410	no	intergenic				3919,2076,432	CC,CT,TT		30.5248,7.9431,22.8723			97098549	9914,2940	2178	4249	6427	SO:0001583	missense	144535	.			GAAAACTTCTTAC																												ENST00000524981.4:c.6503T>C	12.37:g.97098549T>C	ENSP00000431759:p.Leu2168Pro		528	0.0075757576	4		547	0.13	71	.	0		0		Missense_Mutation	SNP	ENST00000524981.4	37		1843	0.8438644688644689	476	0.967479674796748	299	0.8259668508287292	523	0.9143356643356644	545	0.7189973614775725	C	0.045	-1.270654	0.01421	0.920569	0.694752	ENSG00000188596	ENST00000524981;ENST00000342887	.	.	.	4.88	4.88	0.63580	.	0.386776	0.22224	N	0.062913	T	0.00012	0.0000	.	.	.	0.31410	P	0.675574	B	0.02656	0.0	B	0.01281	0.0	T	0.41645	-0.9497	7	0.05833	T	0.94	-7.1488	9.2647	0.37634	0.0:0.9024:0.0:0.0976	rs11108643;rs52829366;rs60573425;rs11108643	593	Q6ZTY8	CL063_HUMAN	P	2168;593	.	ENSP00000345466:L593P	L	+	2	0	C12orf63	95622680	1.000000	0.71417	1.000000	0.80357	0.362000	0.29581	0.906000	0.28517	1.286000	0.44565	-0.226000	0.12346	CTT			0.264	C12orf55-003	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000395046.4			
Unknown	0	bcgsc.ca	37	12	106566174	106566174	+	IGR	SNP	A	A	C	rs3853777	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:106566174A>C								NUAK1 (32363 upstream) : CKAP4 (65480 downstream)																							GTTACCTGACAACAGCGCTGG	0.448													A|||	1525	0.304513	0.0272	0.4654	5008	,	,		17777	0.3462		0.4175	False		,,,				2504	0.4059				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTGACAACAGCG																													12.37:g.106566174A>C			64	0	0		69	0.17	12	.	0		0		RNA	SNP		37																																																																																					0	0.448										
RNF34	80196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	121855684	121855684	+	Silent	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:121855684C>T	ENST00000392464.2	+	3	672	c.603C>T	c.(601-603)gaC>gaT	p.D201D	RNF34_ENST00000361234.5_Silent_p.D201D|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000392465.3_Silent_p.D202D					ring finger protein 34, E3 ubiquitin protein ligase											breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		TGGATGGAGACCAAACATCCA	0.502																																					p.D202D													.	.			0			c.C606T												118.0	136.0	130.0					12																	121855684		2203	4300	6503	SO:0001819	synonymous_variant	80196	exon4			TGGAGACCAAACA	AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"""RING-type (C3HC4) zinc fingers"""	17297	protein-coding gene	gene with protein product		608299	"""ring finger protein 34"""			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.603C>T	12.37:g.121855684C>T			151	0	0		143	0.21	30	NM_194271	124	0.31	38		Silent	SNP	ENST00000392464.2	37																																																																																						0.502	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000413892.1		NM_194271	
CDK2AP1	8099	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	123746287	123746287	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr12:123746287G>T	ENST00000261692.2	-	4	865	c.344C>A	c.(343-345)tCc>tAc	p.S115Y	CDK2AP1_ENST00000544658.1_Missense_Mutation_p.S87Y|CDK2AP1_ENST00000535979.1_Missense_Mutation_p.S87Y|CDK2AP1_ENST00000542174.1_Missense_Mutation_p.S87Y|RP11-282O18.3_ENST00000542427.2_RNA|CDK2AP1_ENST00000538446.1_Missense_Mutation_p.S87Y|RP11-282O18.3_ENST00000543217.2_RNA|RP11-282O18.3_ENST00000544890.1_RNA|RP11-282O18.7_ENST00000602352.1_RNA|RP11-282O18.3_ENST00000541002.3_RNA	NM_001270433.1|NM_001270434.1|NM_004642.3	NP_001257362.1|NP_001257363.1|NP_004633.1	O14519	CDKA1_HUMAN	cyclin-dependent kinase 2 associated protein 1	115					cell cycle (GO:0007049)|DNA-dependent DNA replication (GO:0006261)|positive regulation of protein phosphorylation (GO:0001934)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA polymerase binding (GO:0070182)			lung(2)|stomach(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)		AGGCAGCTAGGATCTGGCATT	0.468																																					p.S115Y													.	.			0			c.C344A												158.0	141.0	147.0					12																	123746287		2203	4300	6503	SO:0001583	missense	8099	exon4			AGCTAGGATCTGG	AB006077	CCDS9245.1, CCDS58289.1	12q24	2008-11-04	2008-11-04		ENSG00000111328	ENSG00000111328			14002	protein-coding gene	gene with protein product		602198	"""CDK2-associated protein 1"""			9331572, 9506968	Standard	NM_004642		Approved	DORC1, doc-1, DOC1, ST19, p12DOC-1	uc001ueq.4	O14519	OTTHUMG00000168854	ENST00000261692.2:c.344C>A	12.37:g.123746287G>T	ENSP00000261692:p.Ser115Tyr		77	0	0		61	0.13	8	NM_004642	466	0.28	131	F5GYA4	Missense_Mutation	SNP	ENST00000261692.2	37	CCDS9245.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798734	0.90538	.	.	ENSG00000111328	ENST00000261692;ENST00000538446;ENST00000535979;ENST00000542174;ENST00000544658	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.80232	0.4585	M	0.73962	2.25	0.58432	D	0.999999	D	0.76494	0.999	D	0.71184	0.972	T	0.81095	-0.1088	9	0.87932	D	0	-18.3923	20.1542	0.98100	0.0:0.0:1.0:0.0	.	115	O14519	CDKA1_HUMAN	Y	115;87;87;87;87	.	ENSP00000261692:S115Y	S	-	2	0	CDK2AP1	122312240	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	9.444000	0.97578	2.767000	0.95098	0.563000	0.77884	TCC			0.468	CDK2AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401387.1		NM_004642	
PSPC1P1	642395	bcgsc.ca	37	13	19801534	19801534	+	IGR	SNP	G	G	A	rs139266746	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:19801534G>A								RP11-408E5.4 (40038 upstream) : RP11-408E5.5 (35402 downstream)																							AGATGCATACGTCCCAGGTTG	0.403													G|||	23	0.00459265	0.0144	0.0043	5008	,	,		21035	0.001		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	642395	.			GCATACGTCCCAG																													13.37:g.19801534G>A			136	0	0		67	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.403										
LINC00621	100996930	bcgsc.ca	37	13	23490250	23490250	+	lincRNA	SNP	C	C	A	rs140913578	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:23490250C>A	ENST00000577004.1	-	0	258				RP11-124N19.3_ENST00000575845.1_lincRNA					long intergenic non-protein coding RNA 621																		AATTTTAAAACAACAGCAAGA	0.393													C|||	840	0.167732	0.1256	0.232	5008	,	,		20369	0.2163		0.165	False		,,,				2504	0.1319				.													.	.			0			.																																											646208	.			TTAAAACAACAGC	AK091626		13q12.12	2012-10-12			ENSG00000262619	ENSG00000262619		"""Long non-coding RNAs"""	44227	non-coding RNA	RNA, long non-coding							Standard			Approved				OTTHUMG00000177835		13.37:g.23490250C>A			233	0.017167382	4		146	0.07	10	.	2	0.00	0		RNA	SNP	ENST00000577004.1	37																																																																																						0.393	LINC00621-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000439167.1			
RFC3	5983	bcgsc.ca	37	13	34540232	34540232	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:34540232G>T	ENST00000434425.1	+	9	998	c.888G>T	c.(886-888)aaG>aaT	p.K296N		NM_181558.2	NP_853536.2	P40938	RFC3_HUMAN	replication factor C (activator 1) 3, 38kDa	296					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to organophosphorus (GO:0046683)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	DNA clamp loader activity (GO:0003689)			lung(2)|skin(1)	3		Hepatocellular(188;0.0191)|Lung SC(185;0.0548)		all cancers(112;5.09e-06)|Epithelial(112;6.52e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00107)|OV - Ovarian serous cystadenocarcinoma(117;0.0285)|GBM - Glioblastoma multiforme(144;0.123)		AGGCATGTAAGGAGGAATCAA	0.378																																					p.K296N													RFC3_ENST00000434425,NS,carcinoma,0,1	RFC3	40	1	0			c.G888T												94.0	91.0	92.0					13																	34540232		1862	4100	5962	SO:0001583	missense	5983	exon9			ATGTAAGGAGGAA		CCDS9352.1, CCDS45025.1	13q13.2	2010-04-21	2002-08-29		ENSG00000133119	ENSG00000133119		"""ATPases / AAA-type"""	9971	protein-coding gene	gene with protein product	"""RFC, 38 kD subunit"", ""A1 38 kDa subunit"""	600405	"""replication factor C (activator 1) 3 (38kD)"""			7774928	Standard	NM_002915		Approved	RFC38, MGC5276	uc001uuz.3	P40938	OTTHUMG00000016715	ENST00000434425.1:c.888G>T	13.37:g.34540232G>T	ENSP00000401001:p.Lys296Asn		63	0	0		46	0.09	4	NM_181558	0		0	C9JU95|O15252|Q5W0E8	Missense_Mutation	SNP	ENST00000434425.1	37	CCDS45025.1	.	.	.	.	.	.	.	.	.	.	G	4.573	0.106456	0.08780	.	.	ENSG00000133119	ENST00000434425	T	0.41065	1.01	3.83	0.169	0.15017	.	.	.	.	.	T	0.21103	0.0508	N	0.08118	0	0.09310	N	1	B	0.18013	0.025	B	0.26770	0.073	T	0.28073	-1.0055	9	0.29301	T	0.29	.	6.3133	0.21176	0.4339:0.0:0.5661:0.0	.	296	C9JU95	.	N	296	ENSP00000401001:K296N	ENSP00000401001:K296N	K	+	3	2	RFC3	33438232	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.214000	0.17541	-0.011000	0.14247	-0.150000	0.13652	AAG			0.378	RFC3-201	KNOWN	basic|CCDS	protein_coding	protein_coding				NM_002915	
NAP1L4P3	730174	bcgsc.ca	37	13	48337965	48337965	+	IGR	SNP	T	T	C	rs9534813	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:48337965T>C								RN7SL700P (304596 upstream) : RP11-279N8.1 (61499 downstream)																							AATGCAATTATGAACCTACAG	0.348													C|||	2303	0.459864	0.2209	0.5303	5008	,	,		20860	0.7312		0.4414	False		,,,				2504	0.4724				.													.	.			0			.																																									SO:0001628	intergenic_variant	730174	.			CAATTATGAACCT																													13.37:g.48337965T>C			119	0	0		55	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.348										
RPL13AP25	100287887	bcgsc.ca	37	13	55015252	55015252	+	IGR	SNP	A	A	C	rs9591591	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:55015252A>C								LINC00458 (308251 upstream) : AL512655.1 (364749 downstream)																							GGACCTCTGGAAGGGCTGGTG	0.582													A|||	840	0.167732	0.1831	0.1643	5008	,	,		15531	0.1012		0.2425	False		,,,				2504	0.1411				.													.	.			0			.																																									SO:0001628	intergenic_variant	100287887	.			CTCTGGAAGGGCT																													13.37:g.55015252A>C			200	0.01	2		142	0.04	6	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.582										
LGMNP1	122199	bcgsc.ca	37	13	65532930	65532930	+	IGR	SNP	A	A	G	rs9598891	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:65532930A>G								LINC00355 (882786 upstream) : AL354775.1 (905374 downstream)																							ATCACCAGGCAGGTGGTTCAT	0.453													A|||	637	0.127196	0.202	0.2104	5008	,	,		21718	0.0437		0.1193	False		,,,				2504	0.0613				.													.	.			0			.																																									SO:0001628	intergenic_variant	122199	.			CCAGGCAGGTGGT																													13.37:g.65532930A>G			75	0	0		33	0.15	5	.	0		0		RNA	SNP		37																																																																																					0	0.453										
MTCL1P1	100288130	bcgsc.ca	37	13	71498338	71498338	+	IGR	SNP	C	C	T	rs7335663	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:71498338C>T								RNU6-54P (464636 upstream) : LINC00348 (90934 downstream)																							GCCCCATTGGCGTGGGCTCAG	0.642													G|||	1842	0.367812	0.2398	0.4726	5008	,	,		18378	0.3919		0.4274	False		,,,				2504	0.3804				.													.	.			0			.																																									SO:0001628	intergenic_variant	100288130	.			CATTGGCGTGGGC																													13.37:g.71498338C>T			105	0	0		68	0.12	8	.	0		0		RNA	SNP		37																																																																																					0	0.642										
MTCL1P1	100288130	bcgsc.ca	37	13	71498360	71498360	+	IGR	SNP	G	G	C	rs7336024	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:71498360G>C								RNU6-54P (464658 upstream) : LINC00348 (90912 downstream)																							GATGTGCAGGGAGGAAGGGGG	0.622													G|||	1842	0.367812	0.2398	0.4726	5008	,	,		18126	0.3919		0.4274	False		,,,				2504	0.3804				.													.	.			0			.																																									SO:0001628	intergenic_variant	100288130	.			TGCAGGGAGGAAG																													13.37:g.71498360G>C			106	0	0		67	0.10	7	.	0		0		RNA	SNP		37																																																																																					0	0.622										
MTCL1P1	100288130	bcgsc.ca	37	13	71498385	71498385	+	IGR	SNP	C	C	T	rs7335686	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:71498385C>T								RNU6-54P (464683 upstream) : LINC00348 (90887 downstream)																							GGCACGCCAGCGAGGCAGGAC	0.622													C|||	1839	0.367212	0.239	0.4726	5008	,	,		18038	0.3899		0.4274	False		,,,				2504	0.3804				.													.	.			0			.																																									SO:0001628	intergenic_variant	100288130	.			CGCCAGCGAGGCA																													13.37:g.71498385C>T			95	0	0		62	0.11	7	.	0		0		RNA	SNP		37																																																																																					0	0.622										
HIGD1AP2	100874450	bcgsc.ca	37	13	81847284	81847284	+	lincRNA	SNP	C	C	A	rs1287528	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:81847284C>A	ENST00000458480.2	+	0	48																											ATCAGGAATTCTGGGAAAAAC	0.388													C|||	1110	0.221645	0.2103	0.1671	5008	,	,		20667	0.3056		0.1849	False		,,,				2504	0.227				.													.	.			0			.																																											100874450	.			GGAATTCTGGGAA																													13.37:g.81847284C>A			35	0	0		27	0.15	4	.	0		0		RNA	SNP	ENST00000458480.2	37																																																																																						0.388	RP11-452B18.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000045393.2			
PEX12P1	121727	bcgsc.ca	37	13	90644911	90644911	+	IGR	SNP	G	G	A	rs9588829	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:90644911G>A								SNORD38 (155420 upstream) : LINC00559 (67594 downstream)																							TGACCGCCCCGCCTACTCCAC	0.493													G|||	953	0.190296	0.1936	0.0965	5008	,	,		18181	0.1458		0.1849	False		,,,				2504	0.3037				.													.	.			0			.																																									SO:0001628	intergenic_variant	121727	.			CGCCCCGCCTACT																													13.37:g.90644911G>A			100	0	0		45	0.13	6	.	0		0		RNA	SNP		37																																																																																					0	0.493										
FAR1P1	100128011	bcgsc.ca	37	13	90823825	90823825	+	IGR	SNP	G	G	T	rs9560569	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:90823825G>T								RNA5SP34 (35730 upstream) : MIR622 (59610 downstream)																							TTTGGAATACGGACAATGTCA	0.333													T|||	2716	0.542332	0.4334	0.5058	5008	,	,		21593	0.62		0.507	False		,,,				2504	0.6718				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128011	.			GAATACGGACAAT																													13.37:g.90823825G>T			59	0	0		37	0.16	6	.	0		0		RNA	SNP		37																																																																																					0	0.333										
FAR1P1	100128011	bcgsc.ca	37	13	90823859	90823859	+	IGR	SNP	C	C	T	rs9555981	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:90823859C>T								RNA5SP34 (35764 upstream) : MIR622 (59576 downstream)																							TCAACTAAACCTTGAAGATAA	0.323													C|||	3132	0.625399	0.733	0.5331	5008	,	,		20930	0.621		0.507	False		,,,				2504	0.6718				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128011	.			CTAAACCTTGAAG																													13.37:g.90823859C>T			59	0	0		36	0.14	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.323										
BRD7P5	100129259	bcgsc.ca	37	13	95411309	95411309	+	IGR	SNP	T	T	A	rs1924075	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:95411309T>A								SOX21-AS1 (42809 upstream) : LINC00557 (200985 downstream)																							ttcccctggatcctgcttctc	0.473													A|||	1793	0.358027	0.6589	0.3458	5008	,	,		18162	0.0972		0.3539	False		,,,				2504	0.2331				.													.	.			0			.																																									SO:0001628	intergenic_variant	100129259	.			CCTGGATCCTGCT																													13.37:g.95411309T>A			52	0	0		36	0.14	5	.	0		0		RNA	SNP		37																																																																																					0	0.473										
BRD7P5	100129259	bcgsc.ca	37	13	95411450	95411450	+	IGR	SNP	A	A	G	rs9516470	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:95411450A>G								SOX21-AS1 (42950 upstream) : LINC00557 (200844 downstream)																							TACTTTGAGGACCAGCCTCAA	0.557													A|||	1574	0.314297	0.5121	0.3242	5008	,	,		14937	0.0962		0.3509	False		,,,				2504	0.227				.													.	.			0			.																																									SO:0001628	intergenic_variant	100129259	.			TTGAGGACCAGCC																													13.37:g.95411450A>G			43	0	0		25	0.20	5	.	0		0		RNA	SNP		37																																																																																					0	0.557										
CLYBL	171425	mdanderson.org	37	13	100258996	100258996	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:100258996C>T	ENST00000376360.1	+	1	74	c.47C>T	c.(46-48)gCg>gTg	p.A16V	CLYBL_ENST00000376354.1_Missense_Mutation_p.A16V|CLYBL_ENST00000376355.3_Missense_Mutation_p.A16V|CLYBL_ENST00000339105.4_Missense_Mutation_p.A16V|CLYBL_ENST00000444838.2_Missense_Mutation_p.A16V			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	16						mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCTGCGGCGGCGGCGCTGCTG	0.771																																					p.A16V													.	.			0			c.C47T												6.0	8.0	7.0					13																	100258996		1853	3611	5464	SO:0001583	missense	171425	exon1			CGGCGGCGGCGCT	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.47C>T	13.37:g.100258996C>T	ENSP00000365538:p.Ala16Val		10	0	0		15	0.20	3	NM_206808	0		0	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	.	.	.	.	.	.	.	.	.	.	C	11.70	1.716201	0.30413	.	.	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105	T;T;T;T;T	0.22945	1.94;1.93;1.94;1.94;1.93	3.41	1.62	0.23740	.	0.402802	0.23706	N	0.045367	T	0.09992	0.0245	N	0.08118	0	0.22500	N	0.999041	B;B;B	0.15473	0.013;0.007;0.004	B;B;B	0.06405	0.001;0.002;0.001	T	0.20806	-1.0264	10	0.28530	T	0.3	.	3.9206	0.09242	0.236:0.6373:0.0:0.1267	.	16;16;16	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	V	16	ENSP00000365533:A16V;ENSP00000365538:A16V;ENSP00000404768:A16V;ENSP00000365532:A16V;ENSP00000342991:A16V	ENSP00000342991:A16V	A	+	2	0	CLYBL	99056997	0.992000	0.36948	0.998000	0.56505	0.553000	0.35397	0.063000	0.14410	0.429000	0.26202	0.313000	0.20887	GCG			0.771	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045611.1			
PARP1P1	144	bcgsc.ca	37	13	111591265	111591265	+	IGR	SNP	G	G	A	rs2239661	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr13:111591265G>A								ANKRD10 (23849 upstream) : LINC00431 (44388 downstream)																							GGGCAGCAGCGACTCTCAGAT	0.542													g|||	1105	0.220647	0.3427	0.1499	5008	,	,		20517	0.2847		0.1223	False		,,,				2504	0.1411				.													.	.			0			.																																									SO:0001628	intergenic_variant	144	.			AGCAGCGACTCTC																													13.37:g.111591265G>A			66	0	0		32	0.16	5	.	0		0		RNA	SNP		37																																																																																					0	0.542										
RANBP20P	326627	bcgsc.ca	37	14	21190932	21190932	+	IGR	SNP	C	C	T	rs60729716	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:21190932C>T								RP11-903H12.3 (15653 upstream) : EDDM3A (23118 downstream)																							CCGATCCTGACGTCCAATATC	0.443													C|||	693	0.138379	0.1846	0.1239	5008	,	,		20696	0.2321		0.0636	False		,,,				2504	0.0665				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCCTGACGTCCAA																													14.37:g.21190932C>T			72	0	0		65	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.443										
Unknown	0	bcgsc.ca	37	14	22070355	22070355	+	IGR	SNP	T	T	C	rs199637760		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:22070355T>C								OR10G3 (31480 upstream) : TRAV1-1 (19635 downstream)																							ACTACCCCGATGTCCACAAAG	0.507																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCCCGATGTCCAC																													14.37:g.22070355T>C			167	0.005988024	1		152	0.13	19	.	0		0		RNA	SNP		37																																																																																					0	0.507										
BRD7P1	100288948	bcgsc.ca	37	14	24219529	24219529	+	IGR	SNP	G	G	A	rs35845573	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:24219529G>A								RP11-388E23.2 (20579 upstream) : RN7SKP205 (41609 downstream)																							CTGTGAGACTGGGAATGACAA	0.448													G|||	392	0.0782748	0.0076	0.1686	5008	,	,		21453	0.001		0.2326	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	100288948	.			GAGACTGGGAATG																													14.37:g.24219529G>A			79	0	0		53	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.448										
FSCB	84075	bcgsc.ca;mdanderson.org	37	14	44975510	44975511	+	Missense_Mutation	DNP	CG	CG	TA	rs372153461|rs45478391|rs3809430	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:44975510_44975511CG>TA	ENST00000340446.4	-	1	971_972	c.680_681CG>TA	c.(679-681)cCG>cTA	p.P227L	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	227						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		CTAAAAGTACCGGGGGACCTTT	0.406																																					p.P227L													.	FSCB	173		0			c.C680T																																									SO:0001583	missense	84075	exon1			AAGTACCGGGGGA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.680_681delinsTA	14.37:g.44975510_44975511delinsTA	ENSP00000344579:p.Pro227Leu		123	0.0081300813	1		97	0.07	7	NM_032135	0		0	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	DNP	ENST00000340446.4	37	CCDS9679.1																																																																																					0.406	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000276788.1		NM_032135	
DOCK11P1	100132537	bcgsc.ca	37	14	45334034	45334034	+	IGR	SNP	T	T	C	rs115079816	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:45334034T>C								RP11-398E10.1 (82002 upstream) : RP11-857B24.1 (12042 downstream)																							ACGTCTTCATTTGAAAGCTTG	0.383													T|||	28	0.00559105	0.0212	0.0	5008	,	,		17953	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTCATTTGAAAG																													14.37:g.45334034T>C			208	0	0		148	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.383										
ZFP64P1	319123	bcgsc.ca	37	14	51171922	51171922	+	IGR	SNP	G	G	A	rs72681673	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:51171922G>A								SAV1 (36873 upstream) : NIN (14558 downstream)																							TAGTCACACAGGTAACACTCG	0.557													G|||	1026	0.204872	0.3071	0.1614	5008	,	,		20214	0.1478		0.1998	False		,,,				2504	0.1616				.													.	.			0			.																																									SO:0001628	intergenic_variant	319123	.			CACACAGGTAACA																													14.37:g.51171922G>A			48	0	0		32	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.557										
DYNLL1P1	246720	bcgsc.ca	37	14	81712844	81712844	+	IGR	SNP	C	C	G	rs12891586	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:81712844C>G								GTF2A1 (25269 upstream) : STON2 (14155 downstream)																							GCGCACTCCACTGAGTTCTGT	0.517													C|||	345	0.0688898	0.0938	0.0663	5008	,	,		22115	0.0099		0.1024	False		,,,				2504	0.0634				.													.	.			0			.																																									SO:0001628	intergenic_variant	246720	.			ACTCCACTGAGTT																													14.37:g.81712844C>G			90	0	0		58	0.07	4	.	0		0		RNA	SNP		37																																																																																					0	0.517										
CHORDC2P	317775	bcgsc.ca	37	14	90204548	90204548	+	RNA	SNP	A	A	G	rs10484019	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:90204548A>G	ENST00000555070.1	-	0	170																											AAGCATCGTGAAAGACTGGAA	0.458													A|||	869	0.173522	0.0915	0.1182	5008	,	,		20156	0.4147		0.1183	False		,,,				2504	0.1319				.													.	.			0			.																																											317775	.			ATCGTGAAAGACT																													14.37:g.90204548A>G			87	0	0		59	0.19	11	.	0		0		RNA	SNP	ENST00000555070.1	37																																																																																						0.458	RP11-33N16.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000411023.1			
ATXN3	4287	hgsc.bcm.edu	37	14	92537354	92537355	+	In_Frame_Ins	INS	-	-	CTGCTGCTGCTGCTGCTGCTG	rs12895357	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:92537354_92537355insCTGCTGCTGCTGCTGCTGCTG	ENST00000532032.1	-	10	924_925	c.915_916insCAGCAGCAGCAGCAGCAGCAG	c.(913-918)cagggg>cagCAGCAGCAGCAGCAGCAGCAGggg	p.304_305insQQQQQQQ	ATXN3_ENST00000502250.1_In_Frame_Ins_p.125_126insQQQQQQQ|ATXN3_ENST00000340660.6_In_Frame_Ins_p.249_250insQQQQQQQ|ATXN3_ENST00000503767.1_In_Frame_Ins_p.289_290insQQQQQQQ|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000545170.1_In_Frame_Ins_p.313_314insQQQQQQQ|ATXN3_ENST00000393287.5_In_Frame_Ins_p.304_305insQQQQQQQ|ATXN3_ENST00000429774.2_In_Frame_Ins_p.297_298insQQQQQQQ			P54252	ATX3_HUMAN	ataxin 3	304	Poly-Gln.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G306R(1)		endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GATAGGTCCCCctgctgctgct	0.446																																					p.G306delinsQQQQQQQG	Esophageal Squamous(190;752 2094 29897 44875 49530)												ATXN3,NS,carcinoma,0,7	ATXN3	46		1	Substitution - Missense(1)	lung(1)	c.916_917insCAGCAGCAGCAGCAGCAGCAG																																									SO:0001652	inframe_insertion	4287	exon10			GGTCCCCCTGCTG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.895_915dupCAGCAGCAGCAGCAGCAGCAG	14.37:g.92537354_92537355insCTGCTGCTGCTGCTGCTGCTG	ENSP00000437157:p.Gln298_Gln304dup		70	0	0		50	0.50	25	NM_004993	38	0.00	0	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	In_Frame_Ins	INS	ENST00000532032.1	37																																																																																						0.446	ATXN3-015	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000388065.1		NM_004993	
IGHA2	3494	bcgsc.ca	37	14	106054108	106054108	+	RNA	SNP	G	G	A	rs12105	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106054108G>A	ENST00000390539.2	-	0	410				AL928742.1_ENST00000581377.1_RNA			P01877	IGHA2_HUMAN	immunoglobulin heavy constant alpha 2 (A2m marker)						antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)										CTCTCAGGCCGGTCAGTGTGC	0.637													.|||	162	0.0323482	0.003	0.0461	5008	,	,		17357	0.0		0.0895	False		,,,				2504	0.0368				.													.	.			0			.							G		66,4180		1,64,2058	35.0	39.0	38.0			-6.7	0.2	14	dbSNP_52	38	676,7784		24,628,3578	no	intergenic				25,692,5636	AA,AG,GG		7.9905,1.5544,5.8398			106054108	742,11964	2123	4230	6353			3494	.			CAGGCCGGTCAGT	J00221		14q32.33	2012-10-02			ENSG00000211890	ENSG00000211890		"""Immunoglobulins / IGH locus"""	5479	other	immunoglobulin gene		147000					Standard	NG_001019		Approved			P01877	OTTHUMG00000152472		14.37:g.106054108G>A			173	0.0057803468	1		139	0.08	11	.	489	0.00	0		RNA	SNP	ENST00000390539.2	37																																																																																						0.637	IGHA2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326338.1		NG_001019	
IGHG2	3501	bcgsc.ca	37	14	106110057	106110057	+	RNA	SNP	G	G	A	rs11160859	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106110057G>A	ENST00000390545.2	-	0	560							P01859	IGHG2_HUMAN	immunoglobulin heavy constant gamma 2 (G2m marker)						complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)										CCTGGTGCACGACGGTGAGGA	0.567													N|||	2179	0.435104	0.1316	0.6484	5008	,	,		23807	0.3869		0.5368	False		,,,				2504	0.6391				.													.	.			0			.							G		1015,3341		128,759,1291	240.0	227.0	232.0			1.1	0.0	14	dbSNP_120	232	4415,4129		1087,2241,944	no	intergenic				1215,3000,2235	AA,AG,GG		48.3263,23.3012,42.093			106110057	5430,7470	2178	4272	6450			3501	.			GTGCACGACGGTG	J00230		14q32.33	2012-10-02			ENSG00000211893	ENSG00000211893		"""Immunoglobulins / IGH locus"""	5526	other	immunoglobulin gene		147110					Standard	NG_001019		Approved			P01859	OTTHUMG00000152482		14.37:g.106110057G>A			186	0.0053763441	1		154	0.06	9	.	3663	0.00	7	A6NE66	RNA	SNP	ENST00000390545.2	37																																																																																						0.567	IGHG2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326391.1		NG_001019	
IGHG2	3501	bcgsc.ca	37	14	106110060	106110060	+	RNA	SNP	G	G	A	rs7146603	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106110060G>A	ENST00000390545.2	-	0	557							P01859	IGHG2_HUMAN	immunoglobulin heavy constant gamma 2 (G2m marker)						complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)										GGTGCACGACGGTGAGGACGC	0.562													N|||	286	0.0571086	0.2073	0.0159	5008	,	,		23781	0.0		0.0	False		,,,				2504	0.001				.													.	.			0			.							G		584,3780		41,502,1639	241.0	227.0	232.0			1.2	0.1	14	dbSNP_116	232	5,8549		0,5,4272	no	intergenic				41,507,5911	AA,AG,GG		0.0585,13.3822,4.5595			106110060	589,12329	2182	4277	6459			3501	.			CACGACGGTGAGG	J00230		14q32.33	2012-10-02			ENSG00000211893	ENSG00000211893		"""Immunoglobulins / IGH locus"""	5526	other	immunoglobulin gene		147110					Standard	NG_001019		Approved			P01859	OTTHUMG00000152482		14.37:g.106110060G>A			185	0	0		159	0.06	9	.	3703	0.00	2	A6NE66	RNA	SNP	ENST00000390545.2	37																																																																																						0.562	IGHG2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326391.1		NG_001019	
IGHA1	3493	bcgsc.ca	37	14	106174123	106174123	+	RNA	SNP	G	G	A	rs141644948	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106174123G>A	ENST00000390547.2	-	0	665							P01876	IGHA1_HUMAN	immunoglobulin heavy constant alpha 1						antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|protein-chromophore linkage (GO:0018298)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)										TGGACCCACCGGATTTTGAGA	0.622													.|||	310	0.061901	0.2269	0.0144	5008	,	,		19165	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.							G		543,3369		37,469,1450	39.0	46.0	44.0			2.5	0.0	14	dbSNP_134	44	4,8272		0,4,4134	no	intergenic				37,473,5584	AA,AG,GG		0.0483,13.8804,4.488			106174123	547,11641	1956	4138	6094			3493	.			CCCACCGGATTTT	J00220		14q32.33	2012-10-02			ENSG00000211895	ENSG00000211895		"""Immunoglobulins / IGH locus"""	5478	other	immunoglobulin gene		146900					Standard	NG_001019		Approved			P01876	OTTHUMG00000152494		14.37:g.106174123G>A			144	0	0		107	0.05	5	.	4409	0.00	6		RNA	SNP	ENST00000390547.2	37																																																																																						0.622	IGHA1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326459.1		NG_001019	
IGHV1-2	28474	bcgsc.ca	37	14	106452817	106452817	+	RNA	SNP	A	A	G	rs1065059	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106452817A>G	ENST00000390594.2	-	0	268									immunoglobulin heavy variable 1-2																		GGGTTGATCCATCCCATCCAC	0.552													.|||	1392	0.277955	0.1952	0.2392	5008	,	,		8986	0.4325		0.1491	False		,,,				2504	0.3906				.													.	.			0			.							A		654,3336		44,566,1385	149.0	145.0	146.0			-3.7	0.0	14	dbSNP_86	146	1245,7083		115,1015,3034	no	intergenic				159,1581,4419	GG,GA,AA		14.9496,16.391,15.4165			106452817	1899,10419	1995	4164	6159			28474	.			TGATCCATCCCAT	X07448		14q32.33	2012-02-08			ENSG00000211934	ENSG00000211934		"""Immunoglobulins / IGH locus"""	5550	other	immunoglobulin gene							Standard	NG_001019		Approved	V35			OTTHUMG00000152320		14.37:g.106452817A>G			685	0.0087591241	6		466	0.05	21	.	520	0.00	2		RNA	SNP	ENST00000390594.2	37																																																																																						0.552	IGHV1-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325882.1		NG_001019	
IGHV3-7	28452	bcgsc.ca	37	14	106518565	106518565	+	RNA	SNP	C	C	T	rs113460079	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106518565C>T	ENST00000390598.2	-	0	264									immunoglobulin heavy variable 3-7																		ACTCCAGCCCCTTCCCTGGAG	0.557													.|||	674	0.134585	0.0643	0.1628	5008	,	,		10025	0.1151		0.171	False		,,,				2504	0.1922				.													.	.			0			.							C		331,3423		13,305,1559	176.0	175.0	175.0			1.9	0.2	14	dbSNP_132	175	1320,6868		110,1100,2884	no	intergenic				123,1405,4443	TT,TC,CC		16.1212,8.8173,13.8252			106518565	1651,10291	1877	4094	5971			28452	.			CAGCCCCTTCCCT	M99649		14q32.33	2012-02-08			ENSG00000211938	ENSG00000211938		"""Immunoglobulins / IGH locus"""	5620	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152271		14.37:g.106518565C>T			808	0.004950495	4		562	0.05	29	.	923	0.00	0		RNA	SNP	ENST00000390598.2	37																																																																																						0.557	IGHV3-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325659.1		NG_001019	
IGHV3-7	28452	bcgsc.ca	37	14	106518848	106518848	+	RNA	SNP	T	T	C	rs2073679	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106518848T>C	ENST00000390598.2	-	0	84									immunoglobulin heavy variable 3-7																		TCAGCCCCAATTCCATGGTGA	0.502													.|||	2294	0.458067	0.584	0.451	5008	,	,		10913	0.3065		0.4274	False		,,,				2504	0.4806				.													.	.			0			.							C		2070,1702		569,932,385	182.0	169.0	173.0			-1.8	0.0	14	dbSNP_96	173	3598,4610		823,1952,1329	no	intergenic				1392,2884,1714	CC,CT,TT		43.8353,45.122,47.3122			106518848	5668,6312	1886	4104	5990			28452	.			CCCCAATTCCATG	M99649		14q32.33	2012-02-08			ENSG00000211938	ENSG00000211938		"""Immunoglobulins / IGH locus"""	5620	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152271		14.37:g.106518848T>C			248	0.0080645161	2		190	0.11	20	.	587	0.01	4		RNA	SNP	ENST00000390598.2	37																																																																																						0.502	IGHV3-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325659.1		NG_001019	
IGHV3-9	28451	bcgsc.ca	37	14	106552310	106552310	+	RNA	SNP	G	G	A	rs8020204	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106552310G>A	ENST00000390600.2	-	0	408									immunoglobulin heavy variable 3-9																		ATACAAGGCCGTGTCCTCAGC	0.532													.|||	657	0.13119	0.438	0.0634	5008	,	,		7571	0.0		0.0169	False		,,,				2504	0.0174				.													.	.			0			.							G		1467,2305		409,649,828	160.0	119.0	133.0			1.4	0.0	14	dbSNP_116	133	198,6902		58,82,3410	no	intergenic				467,731,4238	AA,AG,GG		2.7887,38.8918,15.3146			106552310	1665,9207	1886	3550	5436			28451	.			AAGGCCGTGTCCT	M99651		14q32.33	2012-02-08			ENSG00000211940			"""Immunoglobulins / IGH locus"""	5628	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152291		14.37:g.106552310G>A			220	0	0		143	0.05	7	.	1000	0.00	0		RNA	SNP	ENST00000390600.2	37																																																																																						0.532	IGHV3-9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325679.1		NG_001019	
IGHV3-13	28449	bcgsc.ca	37	14	106586354	106586354	+	RNA	SNP	G	G	C	rs10131161	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106586354G>C	ENST00000390602.2	-	0	210									immunoglobulin heavy variable 3-13																		GGTGAATCCAGAGGCTGCACA	0.572													.|||	659	0.131589	0.4539	0.0562	5008	,	,		10788	0.001		0.0109	False		,,,				2504	0.0082				.													.	.			0			.							G		1386,2372		257,872,750	97.0	92.0	94.0			2.3	0.1	14	dbSNP_119	94	147,8051		8,131,3960	no	intergenic				265,1003,4710	CC,CG,GG		1.7931,36.8813,12.822			106586354	1533,10423	1879	4099	5978			28449	.			AATCCAGAGGCTG	X92217		14q32.33	2012-02-08			ENSG00000211942	ENSG00000211942		"""Immunoglobulins / IGH locus"""	5581	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152295		14.37:g.106586354G>C			93	0	0		66	0.08	5	.	534	0.00	0		RNA	SNP	ENST00000390602.2	37																																																																																						0.572	IGHV3-13-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325683.1		NG_001019	
IGHV3-20	28445	bcgsc.ca;mdanderson.org	37	14	106667810	106667810	+	RNA	SNP	C	C	A	rs112170273	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106667810C>A	ENST00000390606.2	-	0	183				AB019440.50_ENST00000605005.1_lincRNA					immunoglobulin heavy variable 3-20																		AGAGGCTGCACAGGAGAGTCT	0.577													.|||	670	0.133786	0.0272	0.1614	5008	,	,		10054	0.0367		0.2177	False		,,,				2504	0.272				.													.	.			0			.							C		170,3582		5,160,1711	91.0	86.0	88.0			0.8	0.0	14	dbSNP_132	88	1906,6294		250,1406,2444	no	intergenic				255,1566,4155	AA,AC,CC		23.2439,4.5309,17.3695			106667810	2076,9876	1876	4100	5976			28445	.			GCTGCACAGGAGA	M99657		14q32.33	2012-02-08			ENSG00000211946	ENSG00000211946		"""Immunoglobulins / IGH locus"""	5585	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152285		14.37:g.106667810C>A			163	0	0		86	0.17	15	.	34	0.00	0		RNA	SNP	ENST00000390606.2	37																																																																																						0.577	IGHV3-20-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325673.1		NG_001019	
IGHV3-43	28426	bcgsc.ca	37	14	106926311	106926311	+	RNA	SNP	T	T	G	rs4977158|rs539182287	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:106926311T>G	ENST00000434710.1	-	0	310									immunoglobulin heavy variable 3-43																		CTGCATAGTATGTGCTACCAC	0.498													T|||	1026	0.204872	0.2693	0.1354	5008	,	,		21525	0.1647		0.1103	False		,,,				2504	0.3057				.													.	.			0			.							T		779,3213		0,779,1217	242.0	170.0	194.0			2.0	0.0	14	dbSNP_111	194	913,7363		0,913,3225	no	intergenic				0,1692,4442	GG,GT,TT		11.0319,19.514,13.792			106926311	1692,10576	1996	4138	6134			28426	.			ATAGTATGTGCTA	M99672		14q32.33	2012-02-08			ENSG00000232216	ENSG00000232216		"""Immunoglobulins / IGH locus"""	5604	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152094		14.37:g.106926311T>G			159	0	0		121	0.04	5	.	995	0.00	1		RNA	SNP	ENST00000434710.1	37																																																																																						0.498	IGHV3-43-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325191.1		NG_001019	
IGHV5-51	28388	bcgsc.ca	37	14	107035142	107035142	+	RNA	SNP	G	G	A	rs61732461	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107035142G>A	ENST00000390626.2	-	0	79									immunoglobulin heavy variable 5-51																		GGAGGAGGGCGAGGATGGCGG	0.587													g|||	107	0.0213658	0.0	0.0303	5008	,	,		15462	0.001		0.0507	False		,,,				2504	0.0348				.													.	.			0			.												31.0	36.0	34.0					14																	107035142		1989	4162	6151			28388	.			GAGGGCGAGGATG	M99686		14q32.33	2012-02-08			ENSG00000211966	ENSG00000211966		"""Immunoglobulins / IGH locus"""	5659	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151960		14.37:g.107035142G>A			111	0	0		79	0.08	6	.	1700	0.00	2		RNA	SNP	ENST00000390626.2	37																																																																																						0.587	IGHV5-51-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324606.1		NG_001019	
IGHV3-53	28420	bcgsc.ca	37	14	107048767	107048767	+	RNA	SNP	G	G	T	rs200617568		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107048767G>T	ENST00000390627.2	-	0	473									immunoglobulin heavy variable 3-53																		ATGGTGAATCGGCCCTTCACG	0.542																																					.													.	.			0			.												141.0	165.0	157.0					14																	107048767		2174	4286	6460			28420	.			TGAATCGGCCCTT	M99679		14q32.33	2012-02-08			ENSG00000211967	ENSG00000211967		"""Immunoglobulins / IGH locus"""	5610	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151966		14.37:g.107048767G>T			154	0	0		129	0.05	6	.	454	0.00	0		RNA	SNP	ENST00000390627.2	37																																																																																						0.542	IGHV3-53-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324612.1		NG_001019	
IGHV3-64	28414	bcgsc.ca;mdanderson.org	37	14	107113851	107113851	+	RNA	SNP	C	C	T	rs2072045	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107113851C>T	ENST00000454421.2	-	0	320									immunoglobulin heavy variable 3-64																		TTCACAGAGTCTGCATAATAT	0.483													.|||	2874	0.573882	0.7194	0.4524	5008	,	,		19977	0.5337		0.3857	False		,,,				2504	0.6984				.													.	.			0			.							C		2321,1709		616,1089,310	210.0	243.0	232.0			-0.0	0.0	14	dbSNP_96	232	2763,5687		224,2315,1686	no	intergenic				840,3404,1996	TT,TC,CC		32.6982,42.4069,40.7372			107113851	5084,7396	2015	4225	6240			28414	.			CAGAGTCTGCATA	M99682		14q32.33	2012-02-08			ENSG00000223648	ENSG00000223648		"""Immunoglobulins / IGH locus"""	5617	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151971		14.37:g.107113851C>T			119	0	0		87	0.15	13	.	10	0.00	0		RNA	SNP	ENST00000454421.2	37																																																																																						0.483	IGHV3-64-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324617.1		NG_001019	
IGHV3-64	28414	bcgsc.ca	37	14	107114193	107114193	+	RNA	SNP	A	A	G	rs2073670	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107114193A>G	ENST00000454421.2	-	0	81									immunoglobulin heavy variable 3-64																		CCCAAACTCCATCATGACTCT	0.493													.|||	2926	0.584265	0.7564	0.4568	5008	,	,		18482	0.5337		0.3887	False		,,,				2504	0.6953				.													.	.			0			.							A		2526,1214		866,794,210	107.0	109.0	108.0			1.0	0.0	14	dbSNP_96	108	3134,5070		613,1908,1581	no	intergenic				1479,2702,1791	GG,GA,AA		38.2009,32.4599,47.3878			107114193	5660,6284	1870	4102	5972			28414	.			AACTCCATCATGA	M99682		14q32.33	2012-02-08			ENSG00000223648	ENSG00000223648		"""Immunoglobulins / IGH locus"""	5617	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151971		14.37:g.107114193A>G			205	0.0146341463	3		159	0.23	36	.	6	0.00	0		RNA	SNP	ENST00000454421.2	37																																																																																						0.493	IGHV3-64-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324617.1		NG_001019	
IGHV1-69	28461	bcgsc.ca;mdanderson.org	37	14	107170055	107170055	+	RNA	SNP	G	G	A	rs8009570	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107170055G>A	ENST00000390633.2	-	0	287									immunoglobulin heavy variable 1-69																		GTAGTTTGCTGTACCAAAGAT	0.562																																					.													.	.			0			.							G		1332,2826		81,1170,828	248.0	198.0	214.0			-0.5	0.0	14	dbSNP_116	214	3242,5176		604,2034,1571	no	intergenic				685,3204,2399	AA,AG,GG		38.5127,32.0346,36.3709			107170055	4574,8002	2079	4209	6288			28461	.			TTTGCTGTACCAA	L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973		"""Immunoglobulins / IGH locus"""	5558	other	immunoglobulin gene				IGHV1-E		8469934	Standard	NG_001019		Approved				OTTHUMG00000151862		14.37:g.107170055G>A			273	0	0		223	0.05	12	.	6970	0.00	6		RNA	SNP	ENST00000390633.2	37																																																																																						0.562	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324207.1		NG_001019	
IGHV1-69	28461	bcgsc.ca;mdanderson.org	37	14	107170062	107170062	+	RNA	SNP	A	A	G	rs55891010	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107170062A>G	ENST00000390633.2	-	0	280									immunoglobulin heavy variable 1-69																		GCTGTACCAAAGATAGGGATG	0.562													.|||	2234	0.446086	0.3321	0.415	5008	,	,		24277	0.4861		0.3748	False		,,,				2504	0.6544				.													.	.			0			.							G		959,3173		68,823,1175	239.0	190.0	207.0			-0.5	0.0	14	dbSNP_129	207	2812,5598		574,1664,1967	no	intergenic				642,2487,3142	GG,GA,AA		33.4364,23.2091,30.067			107170062	3771,8771	2066	4205	6271			28461	.			TACCAAAGATAGG	L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973		"""Immunoglobulins / IGH locus"""	5558	other	immunoglobulin gene				IGHV1-E		8469934	Standard	NG_001019		Approved				OTTHUMG00000151862		14.37:g.107170062A>G			275	0	0		222	0.06	13	.	6793	0.00	21		RNA	SNP	ENST00000390633.2	37																																																																																						0.562	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324207.1		NG_001019	
IGHV1-69	28461	bcgsc.ca	37	14	107170077	107170077	+	RNA	SNP	C	C	T	rs11845244	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107170077C>T	ENST00000390633.2	-	0	265									immunoglobulin heavy variable 1-69																		GGGATGATCCCTCCCATCCAC	0.562													.|||	2103	0.419928	0.3162	0.4078	5008	,	,		24767	0.4752		0.3628	False		,,,				2504	0.5706				.													.	.			0			.							C		950,3176		76,798,1189	216.0	172.0	186.0			-0.5	0.0	14	dbSNP_120	186	2826,5570		528,1770,1900	no	intergenic				604,2568,3089	TT,TC,CC		33.6589,23.0247,30.1549			107170077	3776,8746	2063	4198	6261			28461	.			TGATCCCTCCCAT	L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973		"""Immunoglobulins / IGH locus"""	5558	other	immunoglobulin gene				IGHV1-E		8469934	Standard	NG_001019		Approved				OTTHUMG00000151862		14.37:g.107170077C>T			293	0.0034129693	1		227	0.05	12	.	7113	0.01	37		RNA	SNP	ENST00000390633.2	37																																																																																						0.562	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324207.1		NG_001019	
IGHV1-69	28461	bcgsc.ca;mdanderson.org	37	14	107170207	107170207	+	RNA	SNP	C	C	T	rs11845287	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107170207C>T	ENST00000390633.2	-	0	135									immunoglobulin heavy variable 1-69																		CAGCCCCAGACTGCACCAGCT	0.562													.|||	840	0.167732	0.1536	0.1671	5008	,	,		25997	0.1677		0.2068	False		,,,				2504	0.1472				.													.	.			0			.							C		565,3303		6,553,1375	107.0	83.0	91.0			0.2	0.0	14	dbSNP_120	91	1556,6720		136,1284,2718	no	intergenic				142,1837,4093	TT,TC,CC		18.8014,14.607,17.4654			107170207	2121,10023	1934	4138	6072			28461	.			CCCAGACTGCACC	L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973		"""Immunoglobulins / IGH locus"""	5558	other	immunoglobulin gene				IGHV1-E		8469934	Standard	NG_001019		Approved				OTTHUMG00000151862		14.37:g.107170207C>T			246	0	0		168	0.07	11	.	9139	0.00	14		RNA	SNP	ENST00000390633.2	37																																																																																						0.562	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324207.1		NG_001019	
IGHV1-69	28461	bcgsc.ca	37	14	107170219	107170219	+	RNA	SNP	C	C	G	rs2187989	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107170219C>G	ENST00000390633.2	-	0	123									immunoglobulin heavy variable 1-69																		GCACCAGCTGCACCTGGGACT	0.552													.|||	3145	0.627995	0.9493	0.4726	5008	,	,		25701	0.504		0.4016	False		,,,				2504	0.6646				.													.	.			0			.							G		3310,536		1428,454,41	99.0	78.0	85.0			-0.5	0.0	14	dbSNP_96	85	3331,4931		704,1923,1504	no	intergenic				2132,2377,1545	GG,GC,CC		40.3171,13.9366,45.152			107170219	6641,5467	1923	4131	6054			28461	.			CAGCTGCACCTGG	L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973		"""Immunoglobulins / IGH locus"""	5558	other	immunoglobulin gene				IGHV1-E		8469934	Standard	NG_001019		Approved				OTTHUMG00000151862		14.37:g.107170219C>G			255	0.0078431373	2		163	0.12	20	.	7831	0.00	4		RNA	SNP	ENST00000390633.2	37																																																																																						0.552	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324207.1		NG_001019	
IGHV2-70	28454	bcgsc.ca	37	14	107179013	107179013	+	RNA	SNP	A	A	G	rs61732216	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107179013A>G	ENST00000390634.2	-	0	239									immunoglobulin heavy variable 2-70																		GATCCAGCTCACACACATTCC	0.547													.|||	12	0.00239617	0.0045	0.0029	5008	,	,		13924	0.004		0.0	False		,,,				2504	0.0				.													.	.			0			.							A		532,3608		1,530,1539	101.0	82.0	88.0			1.6	0.0	14	dbSNP_129	88	1013,7321		50,913,3204	no	intergenic				51,1443,4743	GG,GA,AA		12.155,12.8502,12.3858			107179013	1545,10929	2070	4167	6237			28454	.			CAGCTCACACACA	L21969		14q32.33	2012-02-08			ENSG00000211974	ENSG00000211974		"""Immunoglobulins / IGH locus"""	5577	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151870		14.37:g.107179013A>G			551	0	0		347	0.03	11	.	151	0.00	0		RNA	SNP	ENST00000390634.2	37																																																																																						0.547	IGHV2-70-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324215.1		NG_001019	
IGHV3-73	28409	bcgsc.ca	37	14	107211211	107211211	+	RNA	SNP	G	G	A	rs2073668	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr14:107211211G>A	ENST00000390636.2	-	0	157									immunoglobulin heavy variable 3-73																		AGCCTCCCCCGGACTCCACCA	0.597													.|||	2539	0.506989	0.4902	0.415	5008	,	,		15393	0.5079		0.4076	False		,,,				2504	0.6963				.													.	.			0			.							A		1711,2085		393,925,580	92.0	95.0	94.0			1.1	0.6	14	dbSNP_96	94	3273,4959		688,1897,1531	no	intergenic				1081,2822,2111	AA,AG,GG		39.7595,45.0738,41.4366			107211211	4984,7044	1898	4116	6014			28409	.			TCCCCCGGACTCC	Z27508		14q32.33	2012-02-08			ENSG00000211976	ENSG00000211976		"""Immunoglobulins / IGH locus"""	5623	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151867		14.37:g.107211211G>A			118	0.0084745763	1		88	0.17	15	.	400	0.00	0		RNA	SNP	ENST00000390636.2	37																																																																																						0.597	IGHV3-73-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324212.1		NG_001019	
Unknown	0	bcgsc.ca	37	15	20450317	20450317	+	IGR	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:20450317G>A								RP11-173D3.1 (97111 upstream) : CHEK2P2 (37679 downstream)																							CTGACTCCTCGTGATGAGCCA	0.622																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCCTCGTGATGA																													15.37:g.20450317G>A			154	0	0		189	0.04	8	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.622										
Unknown	0	bcgsc.ca	37	15	20453913	20453913	+	IGR	SNP	C	C	T	rs2601516	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:20453913C>T								RP11-173D3.1 (100707 upstream) : CHEK2P2 (34083 downstream)																							CAGAGGGACACACACCCAGCT	0.612																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGACACACACCC																													15.37:g.20453913C>T			249	0.0120481928	3		208	0.13	27	.	0		0		RNA	SNP		37																																																																																					0	0.612										
Unknown	0	bcgsc.ca	37	15	20467151	20467151	+	IGR	SNP	C	C	T	rs4983660		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:20467151C>T								RP11-173D3.1 (113945 upstream) : CHEK2P2 (20845 downstream)																							CCATCTGCCGCGTGGGTGGGA	0.572																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGCCGCGTGGGT																													15.37:g.20467151C>T			99	0.0101010101	1		109	0.06	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.572										
IGHV1OR15-4	646379	bcgsc.ca	37	15	22482858	22482858	+	IGR	SNP	A	A	G	rs1807224	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:22482858A>G								IGHV4OR15-8 (9505 upstream) : MIR1268A (30370 downstream)																							ATACACGGCCATGTCCTCAGA	0.547																																					.													.	.			0			.							G		2011,2235		234,1543,346	431.0	387.0	402.0			0.9	0.1	15	dbSNP_92	402	4142,4302		565,3012,645	no	intergenic				799,4555,991	GG,GA,AA		49.0526,47.3622,48.487			22482858	6153,6537	2123	4222	6345	SO:0001628	intergenic_variant	646379	.			ACGGCCATGTCCT																													15.37:g.22482858A>G			72	0	0		71	0.08	6	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.547										
Unknown	0	bcgsc.ca	37	15	22691462	22691462	+	IGR	SNP	A	A	G	rs145557440		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:22691462A>G								MIR4509-2 (16221 upstream) : GOLGA8DP (13258 downstream)																							CATCAGCACCATAAGCAATGT	0.502																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	56476	.			AGCACCATAAGCA																													15.37:g.22691462A>G			157	0	0		136	0.06	8	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	15	22691729	22691729	+	IGR	SNP	G	G	C	rs71469079	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:22691729G>C								MIR4509-2 (16488 upstream) : GOLGA8DP (12991 downstream)																							GGGCAAGCGGGATCGGCAAAA	0.507													.|||	613	0.122404	0.1218	0.1138	5008	,	,		49512	0.0109		0.2107	False		,,,				2504	0.1534				.													.	.			0			.																																									SO:0001628	intergenic_variant	56476	.			AAGCGGGATCGGC																													15.37:g.22691729G>C			119	0	0		94	0.07	7	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.507										
NUSAP1	51203	bcgsc.ca	37	15	41634587	41634588	+	Missense_Mutation	DNP	AC	AC	GA	rs386783399|rs7178634|rs7178777	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AC	AC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:41634587_41634588AC>GA	ENST00000559596.1	+	2	184_185	c.97_98AC>GA	c.(97-99)ACc>GAc	p.T33D	NUSAP1_ENST00000558123.1_3'UTR|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T33D|NUSAP1_ENST00000560747.1_Missense_Mutation_p.T33D|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T33D|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T33D|RP11-16O9.2_ENST00000559959.1_RNA|NUSAP1_ENST00000450592.2_Intron|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T33D			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	33			T -> A (in dbSNP:rs7178634).|T -> N (in dbSNP:rs7178777).	T -> D (in Ref. 6; AL833611). {ECO:0000305}.	establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T33N(1)|p.T33A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		CTTGCAGGCAACCAAGTTGTTA	0.342																																					p.T33D													NUSAP1,NS,carcinoma,+1,2	NUSAP1	32	2	2	Substitution - Missense(2)	prostate(2)	c.C98A																																									SO:0001583	missense	51203	exon2			CAGGCAACCAAGT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		Exception_encountered	15.37:g.41634587_41634588delinsGA	ENSP00000453403:p.Thr33Asp		84	0	0		104	0.07	7	NM_018454	208	0.00	0	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	DNP	ENST00000559596.1	37	CCDS45234.1																																																																																					0.342	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000419427.1		NM_016359	
CATSPER2P1	440278	bcgsc.ca	37	15	44020902	44020902	+	IGR	SNP	C	C	T	rs72489216	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:44020902C>T								STRC (10444 upstream) : RNU6-354P (5474 downstream)																							CTCTAGGTTACACTGAAGCTT	0.443													.|||	423	0.0844649	0.0113	0.098	5008	,	,		20151	0.1002		0.17	False		,,,				2504	0.0695				.													.	.			0			.																																									SO:0001628	intergenic_variant	440278	.			AGGTTACACTGAA																													15.37:g.44020902C>T			111	0	0		89	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.443										
Unknown	0	bcgsc.ca	37	15	57848320	57848320	+	IGR	SNP	G	G	A	rs1690317	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:57848320G>A								CGNL1 (5395 upstream) : GCOM1 (35785 downstream)																							TCTTAATTAAGTGGTAGAGAT	0.433													A|||	1203	0.240216	0.3707	0.268	5008	,	,		19980	0.1101		0.2068	False		,,,				2504	0.2127				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AATTAAGTGGTAG																													15.37:g.57848320G>A			22	0	0		16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.433										
HMGN1P26	100128015	bcgsc.ca	37	15	62654429	62654429	+	IGR	SNP	C	C	T	rs2089322	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:62654429C>T								RP11-299H22.7 (77224 upstream) : TLN2 (199134 downstream)																							TTTTTGGCTGCGCTTCCACTT	0.512													C|||	1845	0.368411	0.2027	0.3199	5008	,	,		17050	0.6081		0.2773	False		,,,				2504	0.4734				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGCTGCGCTTCC																													15.37:g.62654429C>T			223	0.0089686099	2		192	0.06	11	.	0		0		RNA	SNP		37																																																																																					0	0.512										
CHRNB4	1143	bcgsc.ca	37	15	79019546	79019546	+	RNA	SNP	C	C	A	rs66615064|rs3829786	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:79019546C>A	ENST00000568337.1	+	0	0																											CCTCCCTCCCCACCCCACGAT	0.562													C|||	1410	0.28155	0.0628	0.4611	5008	,	,		16855	0.372		0.4105	False		,,,				2504	0.2239				.													.	.			0			.																																											0	.			CCTCCCCACCCCA																													15.37:g.79019546C>A			74	0	0		98	0.12	12	.	0		0		RNA	SNP	ENST00000568337.1	37																																																																																						0.562	RP11-160C18.2-004	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000421327.1			
Unknown	0	bcgsc.ca	37	15	79852090	79852090	+	IGR	SNP	C	C	A	rs1765254	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:79852090C>A								KIAA1024 (87458 upstream) : RNU6-667P (257600 downstream)																							CTCCGCGTGCCGGTTTCTCTG	0.517													C|||	2266	0.452476	0.5212	0.5173	5008	,	,		16212	0.3264		0.328	False		,,,				2504	0.5716				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCGTGCCGGTTTC																													15.37:g.79852090C>A			92	0	0		93	0.14	13	.	9	0.00	0		RNA	SNP		37																																																																																					0	0.517										
Unknown	0	bcgsc.ca	37	15	79852517	79852517	+	IGR	SNP	T	T	C	rs138410408	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:79852517T>C								KIAA1024 (87885 upstream) : RNU6-667P (257173 downstream)																							CAGACCAAGGTGAGGAGTCGG	0.597													T|||	41	0.0081869	0.0038	0.0144	5008	,	,		17895	0.0		0.0189	False		,,,				2504	0.0072				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAAGGTGAGGAG																													15.37:g.79852517T>C			158	0.0063291139	1		97	0.09	9	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.597										
ADAMTS7P4	642935	bcgsc.ca	37	15	85806810	85806810	+	IGR	SNP	G	G	A	rs62021386	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:85806810G>A								RP11-561C5.4 (28794 upstream) : RP11-561C5.5 (62814 downstream)																							GTAGGGGGCCGGGGAAGGTGT	0.672													.|||	2923	0.583666	0.7262	0.5764	5008	,	,		17726	0.6438		0.4006	False		,,,				2504	0.5225				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGGCCGGGGAAG																													15.37:g.85806810G>A			64	0	0		53	0.21	11	.	0		0		RNA	SNP		37																																																																																					0	0.672										
Unknown	0	bcgsc.ca	37	15	89532954	89532954	+	IGR	SNP	A	A	G	rs57920986	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:89532954A>G								AC067805.1 (17271 upstream) : RP11-326A19.4 (51499 downstream)																							GCACTTCATTAGACACTGTTA	0.358													A|||	39	0.00778754	0.0295	0.0	5008	,	,		22075	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCATTAGACACT																													15.37:g.89532954A>G			169	0	0		161	0.04	7	.	12	0.00	0		RNA	SNP		37																																																																																					0	0.358										
LRRK1	79705	bcgsc.ca	37	15	101606889	101606890	+	Missense_Mutation	DNP	GC	GC	AA	rs375358524|rs386787404|rs2959197|rs2924835	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr15:101606889_101606890GC>AA	ENST00000388948.3	+	33	6172_6173	c.5813_5814GC>AA	c.(5812-5814)gGC>gAA	p.G1938E	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000532145.1_3'UTR|LRRK1_ENST00000284395.5_Missense_Mutation_p.G1935E	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AAGGATTCTGGCGCCCAGCGGG	0.589																																					p.G1938E													.	LRRK1	310		0			c.C5814A																																									SO:0001583	missense	79705	exon33			ATTCTGGCGCCCA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	Exception_encountered	15.37:g.101606889_101606890delinsAA	ENSP00000373600:p.Gly1938Glu		152	0	0		131	0.05	6	NM_024652	32	0.00	0		Missense_Mutation	DNP	ENST00000388948.3	37	CCDS42086.1																																																																																					0.589	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000384567.2		NM_024652	
IL9RP3	729486	bcgsc.ca	37	16	85561	85561	+	RNA	SNP	C	C	T	rs3930589	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr16:85561C>T	ENST00000568710.1	-	0	0																											GCAGGTACTCCGGGTCCACCA	0.662													.|||	527	0.105232	0.2095	0.098	5008	,	,		20027	0.0268		0.0755	False		,,,				2504	0.0808				.													.	.			0			.																																											729486	.			GTACTCCGGGTCC																													16.37:g.85561C>T			52	0	0		44	0.18	8	.	6	0.00	0		RNA	SNP	ENST00000568710.1	37																																																																																						0.662	Z84812.4-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000420570.1			
Unknown	0	bcgsc.ca	37	16	32941279	32941279	+	IGR	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr16:32941279G>A								RP11-989E6.3 (41330 upstream) : RP11-19N8.2 (22034 downstream)																							TGTCCCAAGGGCATTTGGGGT	0.607																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	647187	.			CCAAGGGCATTTG																													16.37:g.32941279G>A			263	0	0		214	0.04	8	.	0		0		RNA	SNP		37																																																																																					0	0.607										
Unknown	0	bcgsc.ca	37	16	75226838	75226838	+	IGR	SNP	T	T	A	rs1991035	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr16:75226838T>A								ZFP1 (20704 upstream) : CTRB2 (11155 downstream)																							AGCCCTTGGGTCACAGACCAG	0.493													T|||	487	0.0972444	0.0136	0.0836	5008	,	,		24280	0.1429		0.1511	False		,,,				2504	0.1176				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTGGGTCACAGA																													16.37:g.75226838T>A			69	0.0144927536	1		51	0.10	5	.	0		0		RNA	SNP		37																																																																																					0	0.493										
OR1E3	8389	bcgsc.ca	37	17	3019881	3019881	+	IGR	SNP	C	C	T	rs7214748	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:3019881C>T								OR1D2 (23591 upstream) : OR1G1 (9996 downstream)																							TGGACTCCCACCTCCACATGC	0.512													t|||	1031	0.205871	0.5499	0.2104	5008	,	,		23026	0.0317		0.0547	False		,,,				2504	0.0726				.													.	.			0			.																																									SO:0001628	intergenic_variant	8389	.			CTCCCACCTCCAC																													17.37:g.3019881C>T			111	0	0		106	0.06	6	.	0		0		RNA	SNP		37																																																																																					0	0.512										
XAF1	54739	ucsc.edu;bcgsc.ca	37	17	6663894	6663895	+	Missense_Mutation	DNP	GC	GC	AG	rs2271231|rs386794960|rs2271232	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:6663894_6663895GC>AG	ENST00000361842.3	+	4	634_635	c.395_396GC>AG	c.(394-396)cGC>cAG	p.R132Q	XAF1_ENST00000441631.1_Missense_Mutation_p.R132Q|XAF1_ENST00000346752.4_Missense_Mutation_p.R113Q|XAF1_ENST00000438512.1_Missense_Mutation_p.R132Q	NM_017523.3	NP_059993.2	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1	132			R -> H (in dbSNP:rs2271232).	R -> Q (in Ref. 3; BAF85537). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|negative regulation of protein complex assembly (GO:0031333)|response to interferon-beta (GO:0035456)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	6						GATGTCTGTCGCAGTGAACAGG	0.594																																					p.R132Q													XAF1,colon,carcinoma,+2,1	XAF1	16	1	0			c.C396G																																									SO:0001583	missense	54739	exon4			TCTGTCGCAGTGA	X99699	CCDS11080.1, CCDS11081.1	17p13.2	2010-03-19			ENSG00000132530	ENSG00000132530			30932	protein-coding gene	gene with protein product		606717				12029096, 11175744	Standard	NM_199139		Approved	BIRC4BP, XIAPAF1, HSXIAPAF1	uc002gdn.3	Q6GPH4		Exception_encountered	17.37:g.6663894_6663895delinsAG	ENSP00000354822:p.Arg132Gln		298	0.0067114094	2		286	0.11	32	NM_017523	56	0.00	0	A2T931|A2T932|A8K2L1|A8K9Y3|D3DTM6|Q6MZE8|Q8N557|Q99982	Missense_Mutation	DNP	ENST00000361842.3	37	CCDS11080.1																																																																																					0.594	XAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000439643.5		NM_017523	
ZSWIM5P1	100130110	bcgsc.ca	37	17	15672538	15672538	+	IGR	SNP	G	G	A	rs62072425|rs201420644	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:15672538G>A								AC005324.7 (5455 upstream) : RNA5SP436 (13116 downstream)																							GCTGGAAGGCGTGGAGCATGT	0.592													.|||	1637	0.326877	0.2035	0.4179	5008	,	,		22238	0.4653		0.3101	False		,,,				2504	0.3037				.													.	.			0			.																																									SO:0001628	intergenic_variant	100130110	.			GAAGGCGTGGAGC																													17.37:g.15672538G>A			58	0	0		61	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.592										
Unknown	0	bcgsc.ca	37	17	19658853	19658853	+	IGR	SNP	A	A	G	rs11204415	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:19658853A>G								ALDH3A1 (7107 upstream) : ULK2 (15289 downstream)																							CACAGGGGGCAGCCCGTGTGA	0.592													G|||	2454	0.490016	0.6346	0.4092	5008	,	,		17928	0.6329		0.3241	False		,,,				2504	0.3753				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGGGCAGCCCGT																													17.37:g.19658853A>G			32	0	0		48	0.13	6	.	0		0		RNA	SNP		37																																																																																					0	0.592										
Unknown	0	bcgsc.ca	37	17	19659299	19659299	+	IGR	SNP	T	T	C	rs9898251	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:19659299T>C								ALDH3A1 (7553 upstream) : ULK2 (14843 downstream)																							GGAGTCTGGTTGGGGGAACCC	0.622													C|||	2461	0.491414	0.6369	0.4078	5008	,	,		18041	0.6409		0.3231	False		,,,				2504	0.3732				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGGTTGGGGGA																													17.37:g.19659299T>C			23	0	0		27	0.19	5	.	0		0		RNA	SNP		37																																																																																					0	0.622										
RP11-434D2.11	0	broad.mit.edu	37	17	20459625	20459630	+	RNA	DEL	TGGCTG	TGGCTG	-	rs398119751|rs143635700		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TGGCTG	TGGCTG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:20459625_20459630delTGGCTG	ENST00000579603.1	-	0	63																											atttgagggttggctgtgattaatta	0.291																																					.													.	.			0			.																																											0	.			GAGGGTTGGCTGT																													17.37:g.20459625_20459630delTGGCTG			469	0	0		413	0.02	7	.	0		0		RNA	DEL	ENST00000579603.1	37																																																																																						0.291	RP11-434D2.11-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000448286.1			
RNFT1P3	101929203	bcgsc.ca	37	17	20657648	20657648	+	IGR	SNP	T	T	C	rs8064233	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:20657648T>C								AC126365.1 (28691 upstream) : RP11-283C24.1 (33735 downstream)																							GCTATGGACATCTGACCTTAT	0.448													C|||	2135	0.426318	0.7073	0.2305	5008	,	,		19089	0.3274		0.3052	False		,,,				2504	0.4121				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGACATCTGACC																													17.37:g.20657648T>C			52	0	0		47	0.11	5	.	0		0		RNA	SNP		37																																																																																					0	0.448										
NCOR1P2	729490	bcgsc.ca	37	17	21544599	21544599	+	IGR	SNP	A	A	G	rs9912297	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:21544599A>G								AC138710.1 (63428 upstream) : UBBP4 (185001 downstream)																							AGAAACAAGTAAAAGTCtttg	0.289													a|||	1246	0.248802	0.1362	0.2824	5008	,	,		18349	0.3125		0.3062	False		,,,				2504	0.2526				.													.	.			0			.																																									SO:0001628	intergenic_variant	729490	.			ACAAGTAAAAGTC																													17.37:g.21544599A>G			257	0	0		228	0.04	10	.	0		0		RNA	SNP		37																																																																																					0	0.289										
UBBP4	23666	ucsc.edu;bcgsc.ca	37	17	21731041	21731041	+	Missense_Mutation	SNP	G	G	A	rs145087783	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:21731041G>A	ENST00000578713.1	+	1	347	c.343G>A	c.(343-345)Gac>Aac	p.D115N	UBBP4_ENST00000584398.1_3'UTR|UBBP4_ENST00000584755.1_Missense_Mutation_p.D115N|UBBP4_ENST00000583708.1_3'UTR					ubiquitin B pseudogene 4											endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						CATCCCCCCCGACCAGCAGAG	0.552													.|||	920	0.183706	0.0764	0.1628	5008	,	,		20929	0.1587		0.2406	False		,,,				2504	0.3108				.													.	.			0			.																																									SO:0001583	missense	23666	.			CCCCCCGACCAGC	X07499		17p11.2	2011-08-10				ENSG00000263563			12467	pseudogene	pseudogene						2834222	Standard	NG_002285		Approved		uc002gyy.3			ENST00000578713.1:c.343G>A	17.37:g.21731041G>A	ENSP00000464265:p.Asp115Asn		162	0	0		127	0.13	16	.	140	0.00	0		Missense_Mutation	SNP	ENST00000578713.1	37																																																																																						0.552	UBBP4-004	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000444589.2			
TUFMP1	645668	bcgsc.ca	37	17	25409812	25409812	+	IGR	SNP	G	G	A	rs2061899	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:25409812G>A								RP11-260A9.6 (82861 upstream) : RP11-663N22.1 (155072 downstream)																							TCAGGGTGAAGCACTGGCCTT	0.532													a|||	2355	0.470248	0.6369	0.451	5008	,	,		19936	0.506		0.328	False		,,,				2504	0.3681				.													.	.			0			.																																									SO:0001628	intergenic_variant	645668	.			GGTGAAGCACTGG																													17.37:g.25409812G>A			107	0	0		89	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.532										
RAB34	83871	bcgsc.ca	37	17	27043933	27043933	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:27043933G>T	ENST00000395245.3	-	2	760	c.134C>A	c.(133-135)aCa>aAa	p.T45K	RAB34_ENST00000415040.2_Missense_Mutation_p.T45K|RAB34_ENST00000450529.1_Missense_Mutation_p.T45K|RAB34_ENST00000436730.3_Missense_Mutation_p.T45K|RAB34_ENST00000447716.1_Missense_Mutation_p.T102K|RAB34_ENST00000453384.3_Missense_Mutation_p.T102K|RPL23A_ENST00000422514.2_5'Flank|RAB34_ENST00000301043.6_Missense_Mutation_p.T45K|RAB34_ENST00000395243.3_Missense_Mutation_p.T45K|RAB34_ENST00000395242.2_Missense_Mutation_p.T45K	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	45					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CACGGTGCCTGTCCGGTGCTC	0.597																																					p.D192E	Pancreas(175;216 2049 29940 32498 41589)												.	.			0			c.C576A												59.0	62.0	61.0					17																	27043933		2203	4300	6503	SO:0001583	missense	83871	exon2			GTGCCTGTCCGGT	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"""RAB, member RAS oncogene"""	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.134C>A	17.37:g.27043933G>T	ENSP00000378666:p.Thr45Lys		65	0	0		74	0.07	5	NM_001256281	195	0.00	0	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	37	CCDS11240.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.8|21.8	4.202426|4.202426	0.79127|0.79127	.|.	.|.	ENSG00000109113|ENSG00000109113	ENST00000419712|ENST00000453384;ENST00000447716;ENST00000301043;ENST00000395243;ENST00000415040;ENST00000450529;ENST00000395242;ENST00000395245;ENST00000436730;ENST00000412625;ENST00000353676	.|T;T;T;T;T;T;T;T;T	.|0.70282	.|-0.32;-0.1;-0.01;-0.47;0.12;-0.01;-0.01;-0.16;-0.16	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	.|0.047687	.|0.85682	.|D	.|0.000000	T|T	0.73575|0.73575	0.3604|0.3604	M|M	0.69823|0.69823	2.125|2.125	.|0.47245	.|D	.|0.999363	.|P;P;B;B;B;P;B	.|0.44521	.|0.837;0.669;0.052;0.335;0.127;0.554;0.1	.|B;B;B;B;B;B;B	.|0.42462	.|0.388;0.355;0.037;0.058;0.027;0.197;0.036	T|T	0.81169|0.81169	-0.1055|-0.1055	4|9	.|0.72032	.|D	.|0.01	-9.1862|-9.1862	17.8985|17.8985	0.88896|0.88896	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|102;45;45;68;68;45;45	.|E7ES60;E9PEJ9;Q9BZG1-2;C9JI96;B4DNC0;A8MYQ9;Q9BZG1	.|.;.;.;.;.;.;RAB34_HUMAN	K|K	65|102;102;45;45;45;68;45;45;68;45;45	.|ENSP00000413156:T102K;ENSP00000410403:T102K;ENSP00000301043:T45K;ENSP00000378664:T45K;ENSP00000410279:T45K;ENSP00000378663:T45K;ENSP00000378666:T45K;ENSP00000398706:T45K;ENSP00000226259:T45K	.|ENSP00000301043:T45K	Q|T	-|-	1|2	0|0	RAB34|RAB34	24068060|24068060	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.840000|6.840000	0.75369|0.75369	2.812000|2.812000	0.96745|0.96745	0.561000|0.561000	0.74099|0.74099	CAG|ACA			0.597	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000345906.1		NM_031934	
Unknown	0	bcgsc.ca	37	17	27530666	27530666	+	IGR	SNP	C	C	T	rs28419601	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:27530666C>T								MYO18A (23236 upstream) : CRYBA1 (43214 downstream)																							GCAGAGGGCTCTTGCAGCTAG	0.393													-|||	2274	0.454073	0.3865	0.3256	5008	,	,		19135	0.6131		0.4274	False		,,,				2504	0.5				.													.	.			0			.																																									SO:0001628	intergenic_variant	619519	.			AGGGCTCTTGCAG																													17.37:g.27530666C>T			203	0.0049261084	1		170	0.08	13	.	13	0.00	0		RNA	SNP		37																																																																																					0	0.393										
RP11-640N20.6	0	bcgsc.ca	37	17	30415954	30415954	+	RNA	SNP	A	A	G	rs41290974	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:30415954A>G	ENST00000358484.4	+	0	144				RP11-640N20.8_ENST00000581225.1_RNA																							GTCTTTCAATATATCGTATTT	0.249																																					.													.	.			0			.																																											0	.			TTCAATATATCGT																													17.37:g.30415954A>G			409	0.0024449878	1		391	0.06	24	.	0		0		RNA	SNP	ENST00000358484.4	37																																																																																						0.249	RP11-640N20.6-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000447090.1			
LRRC37A11P	342666	bcgsc.ca	37	17	37188445	37188446	+	RNA	DEL	TG	TG	-	rs35288784|rs144191966|rs148983654	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:37188445_37188446delTG	ENST00000425901.2	+	0	2287_2288					NR_033753.2				leucine rich repeat containing 37, member A11, pseudogene																		GAAACCTGACTGAAGTCACAGG	0.475														292	0.0583067	0.0076	0.0461	5008	,	,		22863	0.0188		0.1133	False		,,,				2504	0.1196				.													.	.			0			.																																											342666	.			CCTGACTGAAGTC			17q12	2013-05-14			ENSG00000214553	ENSG00000214553			43815	pseudogene	pseudogene							Standard	NR_033753		Approved		uc002hrd.1		OTTHUMG00000133184		17.37:g.37188445_37188446delTG			74	0	0		62	0.11	7	.	0		0		RNA	DEL	ENST00000425901.2	37																																																																																						0.475	LRRC37A11P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000444105.1		NR_033753	
TMEM99	147184	bcgsc.ca	37	17	38991052	38991053	+	Missense_Mutation	DNP	TT	TT	GA	rs3169915|rs1044806|rs386796999	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TT	TT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:38991052_38991053TT>GA	ENST00000301665.3	+	3	588_589	c.284_285TT>GA	c.(283-285)cTT>cGA	p.L95R		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	95			L -> R (in dbSNP:rs1044806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				AGAGAAGGACTTCTTCTTCCTT	0.47																																					p.L95R													.	TMEM99	21		0			c.T285A																																									SO:0001583	missense	147184	exon3			AAGGACTTCTTCT	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	Exception_encountered	17.37:g.38991052_38991053delinsGA	ENSP00000301665:p.Leu95Arg		187	0.0053475936	1		182	0.07	13	NM_001195386	82	0.00	0	B4DQ34|Q96BP9	Missense_Mutation	DNP	ENST00000301665.3	37	CCDS42319.1																																																																																					0.470	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257681.1		NM_145274	
KRTAP4-16P	85354	bcgsc.ca;mdanderson.org	37	17	39258221	39258221	+	Missense_Mutation	SNP	G	G	A	rs141088836	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:39258221G>A	ENST00000440582.1	-	1	240	c.241C>T	c.(241-243)Ccc>Tcc	p.P81S						keratin associated protein 4-16, pseudogene											haematopoietic_and_lymphoid_tissue(1)|lung(1)	2						CAGCAGCTGGGGTGGCAGCAG	0.667													g|||	31	0.0061901	0.0038	0.0115	5008	,	,		12758	0.0		0.0149	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001583	missense	85354	.			AGCTGGGGTGGCA	AC025904		17q21.2	2013-06-25	2010-01-06	2010-01-06	ENSG00000241241	ENSG00000241241		"""Keratin associated proteins"""	18921	pseudogene	pseudogene			"""keratin associated protein 4 pseudogene 1"""	KRTAP4P1			Standard	NG_005311		Approved	KAP4A			OTTHUMG00000133590	ENST00000440582.1:c.241C>T	17.37:g.39258221G>A	ENSP00000411198:p.Pro81Ser		91	0	0		69	0.12	8	.	0		0		Missense_Mutation	SNP	ENST00000440582.1	37		15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	.	2.368	-0.345038	0.05208	.	.	ENSG00000241241	ENST00000440582	T	0.01406	4.93	2.71	2.71	0.32032	.	.	.	.	.	T	0.01870	0.0059	.	.	.	0.22330	N	0.999193	.	.	.	.	.	.	T	0.45131	-0.9282	6	0.52906	T	0.07	.	11.2069	0.48775	0.0:0.0:1.0:0.0	.	.	.	.	S	81	ENSP00000411198:P81S	ENSP00000411198:P81S	P	-	1	0	AC100808.7	36511747	0.008000	0.16893	0.995000	0.50966	0.149000	0.21700	0.195000	0.17155	1.515000	0.48885	0.184000	0.17185	CCC			0.667	KRTAP4-16P-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000257694.1		NG_005311	
LRRC37A	9884	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	44408722	44408722	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:44408722C>T	ENST00000320254.5	+	9	4082	c.4079C>T	c.(4078-4080)tCa>tTa	p.S1360L	ARL17B_ENST00000434041.2_Intron|LRRC37A_ENST00000496930.1_Missense_Mutation_p.S398L|ARL17B_ENST00000575960.1_Intron|LRRC37A_ENST00000393465.3_Missense_Mutation_p.S1360L|ARL17B_ENST00000575698.1_Intron|ARL17B_ENST00000570618.1_Intron	NM_014834.4	NP_055649.4	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A	1360						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|pancreas(6)|prostate(1)|skin(1)	11		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GGGGCTTTTTCATCCTTAGGA	0.413																																					p.S1360L													.	.			0			c.C4079T												11.0	8.0	10.0					17																	44408722		1605	2017	3622	SO:0001583	missense	9884	exon9			CTTTTTCATCCTT	BC040501	CCDS11504.2	17q21.31	2014-04-01			ENSG00000176681	ENSG00000176681			29069	protein-coding gene	gene with protein product						9628581, 15533724	Standard	NM_014834		Approved	KIAA0563	uc031rbr.1	A6NMS7	OTTHUMG00000149841	ENST00000320254.5:c.4079C>T	17.37:g.44408722C>T	ENSP00000326324:p.Ser1360Leu		80	0	0		106	0.31	33	NM_014834	33	0.09	3	Q68DY2|Q8IWC7	Missense_Mutation	SNP	ENST00000320254.5	37	CCDS11504.2	.	.	.	.	.	.	.	.	.	.	c	11.88	1.770668	0.31320	.	.	ENSG00000176681	ENST00000496930;ENST00000393466;ENST00000393465;ENST00000320254	T;T;T	0.77098	0.45;-1.07;-1.06	2.45	2.45	0.29901	.	.	.	.	.	T	0.81513	0.4838	L	0.42245	1.32	0.23862	N	0.996638	B;D;B	0.76494	0.119;0.999;0.001	B;D;B	0.79108	0.092;0.992;0.003	T	0.67760	-0.5587	9	0.59425	D	0.04	.	8.5564	0.33483	0.0:1.0:0.0:0.0	.	398;480;1360	E9PP10;Q5YKG5;A6NMS7	.;.;L37A1_HUMAN	L	398;1360;1360;1360	ENSP00000437021:S398L;ENSP00000377108:S1360L;ENSP00000326324:S1360L	ENSP00000326324:S1360L	S	+	2	0	LRRC37A	41764483	0.000000	0.05858	0.054000	0.19295	0.038000	0.13279	-0.169000	0.09911	1.672000	0.50884	0.531000	0.56144	TCA			0.413	LRRC37A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000313519.3		NM_014834	
CDC27	996	hgsc.bcm.edu	37	17	45216115	45216115	+	Missense_Mutation	SNP	T	T	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:45216115T>A	ENST00000066544.3	-	13	1787	c.1694A>T	c.(1693-1695)aAt>aTt	p.N565I	CDC27_ENST00000531206.1_Missense_Mutation_p.N571I|CDC27_ENST00000446365.2_Missense_Mutation_p.N504I|CDC27_ENST00000527547.1_Missense_Mutation_p.N564I	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	565					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.N565I(1)|p.N571I(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTCTGGCGAATTTTTATCCAT	0.353																																					p.N571I													CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27_ENST00000531206	0	2	2	Substitution - Missense(2)	ovary(2)	c.A1712T												50.0	55.0	54.0					17																	45216115		2201	4299	6500	SO:0001583	missense	996	exon13			GGCGAATTTTTAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1694A>T	17.37:g.45216115T>A	ENSP00000066544:p.Asn565Ile		73	0.0136986301	1		57	0.05	3	NM_001114091	82	0.00	0	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.271461	0.80469	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.041764	0.85682	D	0.000000	T	0.53997	0.1831	L	0.58810	1.83	0.58432	D	0.999999	D;P;D;P	0.57257	0.979;0.952;0.978;0.914	P;P;P;B	0.56788	0.806;0.546;0.645;0.36	T	0.52019	-0.8631	10	0.37606	T	0.19	-4.6177	13.77	0.63019	0.0:0.0:0.0:1.0	.	504;564;571;565	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	I	565;571;504;564	ENSP00000066544:N565I;ENSP00000434614:N571I;ENSP00000392802:N504I;ENSP00000437339:N564I	ENSP00000066544:N565I	N	-	2	0	CDC27	42571114	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.893000	0.56243	2.141000	0.66446	0.528000	0.53228	AAT			0.353	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000389742.2			
RP11-51L5.7	0	bcgsc.ca	37	17	60361652	60361652	+	5'Flank	SNP	C	C	G	rs139504127	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:60361652C>G	ENST00000602932.1	-	0	0				RP11-51L5.5_ENST00000602493.1_RNA																							CTGTGTTGGACTAGAAGCTGA	0.378													.|||	701	0.139976	0.1157	0.1556	5008	,	,		18016	0.0288		0.2664	False		,,,				2504	0.1462				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			GTTGGACTAGAAG																													17.37:g.60361652C>G	Exception_encountered		361	0.0027700831	1		327	0.13	43	.	0		0		RNA	SNP	ENST00000602932.1	37																																																																																						0.378	RP11-51L5.7-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding		OTTHUMT00000467667.1			
LINC01483	101928122	bcgsc.ca	37	17	67703437	67703437	+	IGR	SNP	C	C	T	rs140678444	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr17:67703437C>T								AC003051.1 (78945 upstream) : AC002539.2 (241564 downstream)																							TTAGTCCATACGGAATAGGTC	0.413													C|||	31	0.0061901	0.0219	0.0029	5008	,	,		16635	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCCATACGGAATA																													17.37:g.67703437C>T			87	0	0		76	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.413										
SDCCAG3P1	388478	bcgsc.ca	37	18	57677294	57677294	+	lincRNA	SNP	A	A	G	rs2000746	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr18:57677294A>G	ENST00000585691.1	+	0	0																											AAGATTCAGTATCTCAGCTCT	0.493													G|||	962	0.192093	0.1876	0.2536	5008	,	,		19463	0.0327		0.2386	False		,,,				2504	0.271				.													.	.			0			.																																											388478	.			TTCAGTATCTCAG																													18.37:g.57677294A>G			65	0	0		62	0.06	4	.	0		0		RNA	SNP	ENST00000585691.1	37																																																																																						0.493	RP11-866E20.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000449078.1			
SERPINB10	5273	bcgsc.ca	37	18	61575232	61575232	+	5'UTR	SNP	A	A	G	rs1006961	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr18:61575232A>G	ENST00000238508.3	+	0	8					NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				ATCTCTTACTACAGGAGCAAA	0.333													A|||	1748	0.349042	0.3669	0.3559	5008	,	,		16452	0.499		0.2296	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001623	5_prime_UTR_variant	5273	.			CTTACTACAGGAG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.-52A>G	18.37:g.61575232A>G			522	0	0		417	0.04	16	.	0		0	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	720	0.32967032967032966	172	0.34959349593495936	118	0.3259668508287293	261	0.4562937062937063	169	0.22295514511873352	A	1.123	-0.654834	0.03480	.	.	ENSG00000242550	ENST00000397996	.	.	.	5.72	-1.56	0.08532	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999845424	.	.	.	.	.	.	T	0.46978	-0.9152	3	.	.	.	.	1.5904	0.02653	0.32:0.2901:0.2708:0.1192	rs1006961;rs1006961	.	.	.	A	196	.	.	T	+	1	0	SERPINB10	59726212	0.198000	0.23374	0.017000	0.16124	0.251000	0.25915	-0.300000	0.08243	-0.521000	0.06426	0.383000	0.25322	ACA			0.333	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000134012.3		NM_005024	
DOT1L	84444	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	2222030	2222030	+	Silent	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:2222030C>T	ENST00000398665.3	+	24	2898	c.2862C>T	c.(2860-2862)gcC>gcT	p.A954A		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	954					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGCCCGGCCTCTCTCACAC	0.682																																					p.A954A													.	.			0			c.C2862T												20.0	27.0	25.0					19																	2222030		1983	4159	6142	SO:0001819	synonymous_variant	84444	exon24			CCCGGCCTCTCTC	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2862C>T	19.37:g.2222030C>T			86	0	0		97	0.12	12	NM_032482	45	0.18	8	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	C	0.345	-0.948028	0.02304	.	.	ENSG00000104885	ENST00000440640	.	.	.	4.32	-8.65	0.00870	.	.	.	.	.	T	0.33469	0.0864	.	.	.	0.37307	D	0.908944	.	.	.	.	.	.	T	0.34875	-0.9811	4	.	.	.	-7.2441	1.8069	0.03082	0.4887:0.1966:0.0948:0.2199	.	.	.	.	L	741	.	.	P	+	2	0	DOT1L	2173030	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	-1.590000	0.02102	-2.278000	0.00677	-0.521000	0.04368	CCT			0.682	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318066.1		NM_032482	
DENND1C	79958	bcgsc.ca	37	19	6470310	6470310	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:6470310C>T	ENST00000381480.2	-	18	1470	c.1358G>A	c.(1357-1359)cGc>cAc	p.R453H	DENND1C_ENST00000543576.1_Missense_Mutation_p.R409H	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	453					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CCTCACCGAGCGGTACATGTT	0.597																																					p.R453H													.	DENND1C	93		0			c.G1358A												42.0	47.0	46.0					19																	6470310		2061	4187	6248	SO:0001583	missense	79958	exon18			ACCGAGCGGTACA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1358G>A	19.37:g.6470310C>T	ENSP00000370889:p.Arg453His		155	0	0		119	0.06	7	NM_024898	22	0.00	0	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	C	19.27	3.795005	0.70452	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11821	2.91;2.74	4.99	4.99	0.66335	.	0.192145	0.32703	N	0.005751	T	0.31420	0.0796	L	0.53249	1.67	0.35075	D	0.762834	D	0.76494	0.999	D	0.64410	0.925	T	0.39881	-0.9592	10	0.87932	D	0	-26.9138	15.752	0.77992	0.0:1.0:0.0:0.0	.	453	Q8IV53	DEN1C_HUMAN	H	453;409	ENSP00000370889:R453H;ENSP00000437805:R409H	ENSP00000370889:R453H	R	-	2	0	DENND1C	6421310	1.000000	0.71417	1.000000	0.80357	0.502000	0.33828	2.461000	0.45040	2.313000	0.78055	0.455000	0.32223	CGC			0.597	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000453332.2		NM_024898	
AP1M2	10053	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	10694299	10694299	+	Missense_Mutation	SNP	G	G	C			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:10694299G>C	ENST00000250244.6	-	3	332	c.250C>G	c.(250-252)Ctg>Gtg	p.L84V	AP1M2_ENST00000590923.1_Missense_Mutation_p.L84V	NM_005498.4	NP_005489.2	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	84					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein targeting (GO:0006605)|regulation of defense response to virus by virus (GO:0050690)|vesicle targeting (GO:0006903)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				endometrium(4)|large_intestine(1)|lung(1)|ovary(2)|urinary_tract(1)	9			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			GTCTTATACAGGAAGGAGTAC	0.483																																					p.L84V													.	.			0			c.C250G												139.0	139.0	139.0					19																	10694299		1999	4152	6151	SO:0001583	missense	10053	exon3			TATACAGGAAGGA	AF020797	CCDS45964.1	19p13.2	2008-10-07				ENSG00000129354			558	protein-coding gene	gene with protein product		607309				10338135	Standard	NM_005498		Approved	HSMU1B, mu2, AP1-mu2	uc002mpc.3	Q9Y6Q5		ENST00000250244.6:c.250C>G	19.37:g.10694299G>C	ENSP00000250244:p.Leu84Val		142	0	0		124	0.08	10	NM_005498	126	0.22	28	B2RDV5|Q9BSI8	Missense_Mutation	SNP	ENST00000250244.6	37	CCDS45964.1	.	.	.	.	.	.	.	.	.	.	g	13.00	2.107500	0.37145	.	.	ENSG00000129354	ENST00000250244	T	0.80033	-1.33	4.99	2.88	0.33553	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.64402	D	0.000001	D	0.91274	0.7249	H	0.96916	3.905	0.58432	D	0.999998	D;P	0.71674	0.998;0.925	D;P	0.64321	0.924;0.706	D	0.91466	0.5193	10	0.62326	D	0.03	-34.2148	10.1888	0.43013	0.1638:0.0:0.8362:0.0	.	84;84	Q9Y6Q5-2;Q9Y6Q5	.;AP1M2_HUMAN	V	84	ENSP00000250244:L84V	ENSP00000250244:L84V	L	-	1	2	AP1M2	10555299	1.000000	0.71417	0.996000	0.52242	0.017000	0.09413	3.568000	0.53820	0.713000	0.32060	0.591000	0.81541	CTG			0.483	AP1M2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000452034.1			
ZNF849P	100130108	bcgsc.ca	37	19	22868096	22868096	+	RNA	SNP	A	A	G	rs55716469	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22868096A>G	ENST00000601860.1	-	0	340																		p.Q43R(1)									GAAAATTTACAGTTAGGAAAA	0.338													a|||	621	0.124002	0.09	0.1052	5008	,	,		16452	0.1736		0.1272	False		,,,				2504	0.1288				.													ENSG00000198153,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	stomach(1)	.																																											0	.			ATTTACAGTTAGG																													19.37:g.22868096A>G			164	0	0		159	0.05	8	.	0		0		Missense_Mutation	SNP	ENST00000601860.1	37		292	0.1336996336996337	48	0.0975609756097561	47	0.1298342541436464	105	0.18356643356643357	92	0.12137203166226913	.	10.14	1.267714	0.23136	.	.	ENSG00000198153	ENST00000340708	.	.	.	0.819	0.819	0.18785	.	.	.	.	.	T	0.00109	0.0003	.	.	.	.	.	.	.	.	.	.	.	.	T	0.09400	-1.0676	4	0.56958	D	0.05	.	5.5601	0.17140	1.0:0.0:0.0:0.0	rs55716469;rs62120294	.	.	.	R	43	.	ENSP00000342595:Q43R	Q	+	2	0	AC011467.1	22659936	0.000000	0.05858	0.082000	0.20525	0.080000	0.17528	0.072000	0.14617	0.243000	0.21327	0.240000	0.17902	CAG			0.338	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF849P	100130108	bcgsc.ca	37	19	22868205	22868205	+	RNA	SNP	T	T	C	rs597906	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22868205T>C	ENST00000601860.1	-	0	340																		p.D79D(1)									TACAATGTGATAAATATGTGA	0.308													c|||	1070	0.213658	0.407	0.134	5008	,	,		16794	0.1756		0.1352	False		,,,				2504	0.1288				.													ENSG00000198153,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.																																											0	.			ATGTGATAAATAT																													19.37:g.22868205T>C			173	0	0		146	0.08	11	.	0		0		Silent	SNP	ENST00000601860.1	37																																																																																						0.308	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF849P	100130108	bcgsc.ca	37	19	22868445	22868445	+	RNA	SNP	C	C	T	rs56224405	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22868445C>T	ENST00000601860.1	-	0	340																		p.P159P(1)									GAAAGAAACCCTACAAATGCG	0.388																																					.													ENSG00000198153,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.																																											0	.			GAAACCCTACAAA																													19.37:g.22868445C>T			673	0.0014858841	1		581	0.03	15	.	0		0		Silent	SNP	ENST00000601860.1	37																																																																																						0.388	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF849P	100130108	bcgsc.ca	37	19	22868541	22868541	+	RNA	SNP	G	G	A	rs56356904	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22868541G>A	ENST00000601860.1	-	0	340																		p.E191E(1)									ACATATGTGAGGACTGTGGCA	0.398													g|||	1068	0.213259	0.4062	0.134	5008	,	,		18595	0.1736		0.1362	False		,,,				2504	0.1288				.													ENSG00000198153,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.																																											0	.			ATGTGAGGACTGT																													19.37:g.22868541G>A			353	0	0		311	0.04	12	.	1	0.00	0		Silent	SNP	ENST00000601860.1	37																																																																																						0.398	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF849P	100130108	bcgsc.ca	37	19	22869030	22869030	+	RNA	SNP	G	G	A	rs78524936	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22869030G>A	ENST00000601860.1	-	0	340																		p.K354K(1)									CTGGAGAGAAGCCCTACAAAT	0.378													a|||	1030	0.205671	0.3812	0.1311	5008	,	,		18532	0.1736		0.1332	False		,,,				2504	0.1288				.													ENSG00000198153,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.																																											0	.			AGAGAAGCCCTAC																													19.37:g.22869030G>A			531	0.0018832392	1		420	0.06	26	.	0		0		Silent	SNP	ENST00000601860.1	37																																																																																						0.378	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF849P	100130108	bcgsc.ca	37	19	22869372	22869372	+	RNA	SNP	C	C	T	rs35689937	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:22869372C>T	ENST00000601860.1	-	0	340																											AGAAACCCTACAAGTGTGAAG	0.393													c|||	189	0.0377396	0.0295	0.0187	5008	,	,		19533	0.0813		0.0388	False		,,,				2504	0.0164				.													.	.			0			.																																											0	.			ACCCTACAAGTGT																													19.37:g.22869372C>T			157	0	0		125	0.08	10	.	0		0		Silent	SNP	ENST00000601860.1	37																																																																																						0.393	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF91	7644	bcgsc.ca	37	19	23542290	23542291	+	Missense_Mutation	DNP	AG	AG	GC	rs368101335|rs386808073|rs428549|rs385750	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:23542290_23542291AG>GC	ENST00000300619.7	-	4	3695_3696	c.3490_3491CT>GC	c.(3490-3492)CTa>GCa	p.L1164A	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.L1132A|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1164			L -> P (in dbSNP:rs428549).|L -> V (in dbSNP:rs385750).	L -> A (in Ref. 2; BAF83945). {ECO:0000305}.	transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ctcccaaagtagtgggattaca	0.426																																					p.L1164A													.	ZNF91	349		0			c.C3490G																																									SO:0001583	missense	7644	exon4			CAAAGTAGTGGGA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3490_3491delinsGC	19.37:g.23542290_23542291delinsGC	ENSP00000300619:p.Leu1164Ala		46	0	0		57	0.11	6	NM_003430	20	0.00	0	A8K5E1|B7Z6G6	Missense_Mutation	DNP	ENST00000300619.7	37	CCDS42541.1																																																																																					0.426	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000465891.1		NM_003430	
CAPNS1	826	bcgsc.ca	37	19	36640664	36640669	+	Intron	DEL	GCTGGT	GCTGGT	-	rs145937393|rs17879265	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GCTGGT	GCTGGT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:36640664_36640669delGCTGGT	ENST00000246533.3	+	11	1378				CAPNS1_ENST00000588815.1_Intron|CAPNS1_ENST00000590874.1_Intron|CAPNS1_ENST00000587718.1_In_Frame_Del_p.LV303del|CAPNS1_ENST00000588780.1_Intron|AD001527.7_ENST00000604228.1_RNA|CAPNS1_ENST00000589146.1_Intron	NM_001003962.1|NM_001749.2	NP_001003962.1|NP_001740.1	P04632	CPNS1_HUMAN	calpain, small subunit 1						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GGGCAAAGGGGCTGGTGCTCTTGGGG	0.631														52	0.0103834	0.0008	0.0173	5008	,	,		17428	0.0		0.0338	False		,,,				2504	0.0051				.	Esophageal Squamous(129;1541 1691 5780 18353 34150)												.	CAPNS1	19		0			.								,	36,4228		2,32,2098					,	-2.8	0.0		dbSNP_124	83	249,8005		8,233,3886	no	intron,intron	CAPNS1	NM_001749.2,NM_001003962.1	,	10,265,5984	A1A1,A1R,RR		3.0167,0.8443,2.2767	,	,		285,12233				SO:0001627	intron_variant	826	.			AAAGGGGCTGGTG	X04106	CCDS12489.1	19q13.1	2013-01-10		2001-08-10	ENSG00000126247	ENSG00000126247	3.4.22.52	"""EF-hand domain containing"""	1481	protein-coding gene	gene with protein product		114170		CAPN4		3024120, 3016651	Standard	NM_001003962		Approved	CANP, CANPS, 30K, CDPS	uc002odj.3	P04632		ENST00000246533.3:c.781-46GCTGGT>-	19.37:g.36640664_36640669delGCTGGT			132	0	0		141	0.04	5	.	3	0.00	0	A8K0P1|Q8WTX3|Q96EW0	In_Frame_Del	DEL	ENST00000246533.3	37	CCDS12489.1																																																																																					0.631	CAPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000457411.2			
RAB4B	53916	hgsc.bcm.edu	37	19	41285813	41285813	+	Intron	SNP	C	C	T	rs61750952	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:41285813C>T	ENST00000594800.1	+	2	176				RAB4B_ENST00000357052.2_Intron|RAB4B-EGLN2_ENST00000594136.1_Intron|MIA-RAB4B_ENST00000600729.1_Intron|RAB4B-EGLN2_ENST00000601949.1_Intron|RAB4B_ENST00000602069.1_Intron			P61018	RAB4B_HUMAN	RAB4B, member RAS oncogene family						glucose import (GO:0046323)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	insulin-responsive compartment (GO:0032593)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	GTP binding (GO:0005525)			endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	11			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			ATGTCTGTTTCTCTCCCTCTA	0.398																																					.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CTGTTTCTCTCCC	AF165522	CCDS33030.1	19q13.2	2012-10-15			ENSG00000167578	ENSG00000167578		"""RAB, member RAS oncogene"""	9782	protein-coding gene	gene with protein product	"""ras-related GTP-binding protein 4b"", ""small GTP binding protein RAB4B"""	612945					Standard	NM_016154		Approved	FLJ78649, MGC52123	uc002opd.2	P61018		ENST00000594800.1:c.17-111C>T	19.37:g.41285813C>T			83	0	0		68	0.09	6	.	0		0	P22750|Q7Z514|Q9HBR6	RNA	SNP	ENST00000594800.1	37	CCDS33030.1																																																																																					0.398	RAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000463168.1		NM_016154	
TMEM91	641649	bcgsc.ca	37	19	41888851	41888861	+	Intron	DEL	GGGGACTGGGC	GGGGACTGGGC	-	rs138731997|rs369679620	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GGGGACTGGGC	GGGGACTGGGC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:41888851_41888861delGGGGACTGGGC	ENST00000392002.2	+	3	1020				TMEM91_ENST00000413014.2_Intron|CTC-435M10.3_ENST00000540732.1_Intron|TMEM91_ENST00000356385.4_Intron|TMEM91_ENST00000544232.1_Intron|CTC-435M10.3_ENST00000604424.1_Intron|TMEM91_ENST00000604123.1_Intron|BCKDHA_ENST00000595085.1_Intron|TMEM91_ENST00000447302.2_Intron|TMEM91_ENST00000542945.1_Frame_Shift_Del_p.GDWA129fs|TMEM91_ENST00000539627.1_Frame_Shift_Del_p.GDWA129fs|TMEM91_ENST00000436170.2_Intron	NM_001098821.1	NP_001092291.1	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91						hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						GGGACTTGGAGGGGACTGGGCATAAAAGAGA	0.531														414	0.0826677	0.028	0.0793	5008	,	,		20818	0.0466		0.1312	False		,,,				2504	0.1462				.													.	TMEM91	22		0			.								,,,,,	128,3724		3,122,1801					,,,,,	2.4	0.6		dbSNP_134	228	1093,6889		86,921,2984	no	intron,intron,intron,intron,intron,intron	TMEM91	NM_001098825.1,NM_001098824.1,NM_001098823.1,NM_001098822.1,NM_001098821.1,NM_001042595.2	,,,,,	89,1043,4785	A1A1,A1R,RR		13.6933,3.3229,10.3177	,,,,,	,,,,,		1221,10613				SO:0001627	intron_variant	641649	.			CTTGGAGGGGACT	AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16							32393	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 6"""					12477932	Standard	NM_001098824		Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000392002.2:c.360+25GGGGACTGGGC>-	19.37:g.41888851_41888861delGGGGACTGGGC			133	0	0		82	0.07	6	.	6	0.00	0	C9J9D1|C9JZ62|C9K046|Q6P434	Frame_Shift_Del	DEL	ENST00000392002.2	37	CCDS42571.1																																																																																					0.531	TMEM91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398302.2			
PSG3	5671	bcgsc.ca	37	19	43243217	43243218	+	Missense_Mutation	DNP	AA	AA	GG	rs34721205|rs12185497|rs12185496	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:43243217_43243218AA>GG	ENST00000327495.5	-	2	272_273	c.88_89TT>CC	c.(88-90)TTg>CCg	p.L30P	PSG3_ENST00000595140.1_Missense_Mutation_p.L30P|PSG3_ENST00000490592.1_5'UTR	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	30			L -> P (in dbSNP:rs12185496). {ECO:0000269|PubMed:2302228, ECO:0000269|PubMed:2341148, ECO:0000269|PubMed:2350345, ECO:0000269|PubMed:3265688}.|L -> S (in dbSNP:rs12185496).		defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.L30L(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				AGTGGTAGGCAAGTTCCAGAAG	0.48																																					p.L30P													PSG3,NS,carcinoma,0,1	PSG3	82	1	1	Substitution - coding silent(1)	stomach(1)	c.T88C																																									SO:0001583	missense	5671	exon2			GTAGGCAAGTTCC		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.88_89delinsGG	19.37:g.43243217_43243218delinsGG	ENSP00000332215:p.Leu30Pro		181	0.0055248619	1		139	0.09	12	NM_021016	0		0	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	DNP	ENST00000327495.5	37	CCDS12611.1																																																																																					0.480	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000321423.2		NM_021016	
CD177P1	653579	bcgsc.ca	37	19	43883273	43883273	+	IGR	SNP	G	G	C	rs113172076	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:43883273G>C								CTC-490G23.4 (10151 upstream) : TEX101 (22374 downstream)																							AAGGATCCTGGGTCTAGGGAA	0.547													G|||	471	0.0940495	0.0915	0.1037	5008	,	,		18617	0.0		0.171	False		,,,				2504	0.1084				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCCTGGGTCTAG																													19.37:g.43883273G>C			60	0	0		48	0.10	5	.	1	0.00	0		Missense_Mutation	SNP		37		218	0.09981684981684982	56	0.11382113821138211	43	0.11878453038674033	0	0.0	119	0.15699208443271767	g	11.93	1.786737	0.31593	.	.	ENSG00000204933	ENST00000378007	T	0.27104	1.69	2.17	2.17	0.27698	.	.	.	.	.	T	0.00144	0.0004	.	.	.	.	.	.	.	.	.	.	.	.	T	0.09357	-1.0678	5	0.87932	D	0	.	7.8989	0.29723	0.0:0.0:1.0:0.0	.	.	.	.	A	2	ENSP00000367246:P2A	ENSP00000367246:P2A	P	-	1	0	AC005392.1	48575113	0.004000	0.15560	0.004000	0.12327	0.017000	0.09413	0.771000	0.26633	1.537000	0.49254	0.491000	0.48974	CCA		0	0.547										
ZNF180	7733	bcgsc.ca	37	19	44977071	44977071	+	IGR	SNP	C	C	T	rs1897824	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:44977071C>T	ENST00000221327.4	-	0	3126				AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AAGGATTTTGCGTATAGCTCT	0.413													T|||	1494	0.298323	0.5666	0.2406	5008	,	,		24078	0.0724		0.3469	False		,,,				2504	0.1595				.	Esophageal Squamous(180;1353 2003 32862 46574 49854)												.	.			0			.																																									SO:0001628	intergenic_variant	147711	.			ATTTTGCGTATAG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8			19.37:g.44977071C>T			163	0.0061349693	1		120	0.16	19	.	0		0	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	RNA	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																					0.413	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000451601.1		NM_013256	
ZNF180	7733	bcgsc.ca	37	19	44977240	44977240	+	IGR	SNP	A	A	G	rs1897823	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:44977240A>G	ENST00000221327.4	-	0	3126				AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GACTTCAGTCAGAATTCAGAT	0.408													a|||	2176	0.434505	0.6225	0.2939	5008	,	,		21804	0.4335		0.4503	False		,,,				2504	0.2648				.	Esophageal Squamous(180;1353 2003 32862 46574 49854)												.	.			0			.																																									SO:0001628	intergenic_variant	147711	.			TCAGTCAGAATTC	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8			19.37:g.44977240A>G			62	0	0		67	0.12	8	.	0		0	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	RNA	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																					0.408	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000451601.1		NM_013256	
ZNF180	7733	bcgsc.ca	37	19	44977262	44977262	+	IGR	SNP	T	T	C	rs17714261	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:44977262T>C	ENST00000221327.4	-	0	3126				AC069278.4_ENST00000591684.1_lincRNA	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TTCGTGTTCATCTCAGAGTCC	0.423													T|||	378	0.0754792	0.0098	0.0879	5008	,	,		21545	0.002		0.2276	False		,,,				2504	0.0746				.	Esophageal Squamous(180;1353 2003 32862 46574 49854)												.	.			0			.																																									SO:0001628	intergenic_variant	147711	.			TGTTCATCTCAGA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8			19.37:g.44977262T>C			61	0.0163934426	1		71	0.11	8	.	0		0	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	RNA	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																					0.423	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000451601.1		NM_013256	
LMTK3	114783	bcgsc.ca	37	19	49012706	49012706	+	Silent	SNP	G	G	C			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:49012706G>C	ENST00000600059.1	-	4	653	c.426C>G	c.(424-426)ggC>ggG	p.G142G	LMTK3_ENST00000270238.3_Silent_p.G171G			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	142	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		TCCCAAACCAGCCACTCCCAA	0.632																																					p.G171G													.	LMTK3	125		0			c.C513G												20.0	25.0	23.0					19																	49012706		2003	4115	6118	SO:0001819	synonymous_variant	114783	exon5			AAACCAGCCACTC	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.426C>G	19.37:g.49012706G>C			310	0.0032258065	1		197	0.07	13	NM_001080434	0		0	Q4G0U1	Silent	SNP	ENST00000600059.1	37																																																																																						0.632	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000466137.1		NM_052895	
Unknown	0	bcgsc.ca	37	19	50222914	50222914	+	IGR	SNP	G	G	A	rs3810261	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:50222914G>A								CPT1C (5926 upstream) : TSKS (20097 downstream)																							CGGGATGTTCGCCACCTGATT	0.637													a|||	1069	0.213458	0.2368	0.2378	5008	,	,		17557	0.2897		0.1034	False		,,,				2504	0.1994				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGTTCGCCACCT																													19.37:g.50222914G>A			38	0	0		44	0.20	9	.	2	1.00	2		RNA	SNP		37																																																																																					0	0.637										
Unknown	0	bcgsc.ca	37	19	50222955	50222955	+	IGR	SNP	T	T	C	rs1812666	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:50222955T>C								CPT1C (5967 upstream) : TSKS (20056 downstream)																							GGCGGATCAGTACGCCAGCGT	0.572													N|||	1365	0.272564	0.5159	0.2939	5008	,	,		17150	0.2669		0.0209	False		,,,				2504	0.1933				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GATCAGTACGCCA																													19.37:g.50222955T>C			50	0	0		43	0.12	5	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.572										
MYH14	79784	hgsc.bcm.edu	37	19	50714016	50714016	+	Missense_Mutation	SNP	G	G	T	rs199910006		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:50714016G>T	ENST00000596571.1	+	1	394	c.394G>T	c.(394-396)Ggc>Tgc	p.G132C	MYH14_ENST00000601313.1_Missense_Mutation_p.G132C|MYH14_ENST00000376970.2_Missense_Mutation_p.G132C|MYH14_ENST00000440075.2_Missense_Mutation_p.G132C|MYH14_ENST00000262269.8_Missense_Mutation_p.G132C|MYH14_ENST00000425460.1_Missense_Mutation_p.G132C|MYH14_ENST00000598205.1_Missense_Mutation_p.G132C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	132	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GTACTACTCCGGCCTCATCTA	0.657																																					p.G132C													.	.			0			c.G394T												15.0	18.0	17.0					19																	50714016		2180	4276	6456	SO:0001583	missense	79784	exon2			TACTCCGGCCTCA	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.394G>T	19.37:g.50714016G>T	ENSP00000472819:p.Gly132Cys		75	0	0		67	0.06	4	NM_001077186	15	0.00	0	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420298	0.62622	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	4.29	3.26	0.37387	Myosin head, motor domain (2);	.	.	.	.	D	0.87297	0.6142	M	0.92459	3.31	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.986;0.995;0.995	D	0.88403	0.3016	9	0.66056	D	0.02	.	9.9485	0.41626	0.104:0.0:0.896:0.0	.	132;132;132	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	132	ENSP00000406273:G132C;ENSP00000366169:G132C;ENSP00000407879:G132C;ENSP00000262269:G132C	ENSP00000262269:G132C	G	+	1	0	MYH14	55405828	1.000000	0.71417	0.981000	0.43875	0.964000	0.63967	5.354000	0.66040	2.392000	0.81423	0.555000	0.69702	GGC			0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000464710.2		NM_024729	
RFPL4A	342931	bcgsc.ca;mdanderson.org	37	19	56274424	56274424	+	Silent	SNP	C	C	A	rs150161449		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:56274424C>A	ENST00000434937.2	+	3	918	c.747C>A	c.(745-747)ccC>ccA	p.P249P		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	249	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTTGCGAGCCCTGGCGTCCAT	0.463																																					p.P249P													.	RFPL4A	8		0			c.C747A												102.0	91.0	95.0					19																	56274424		692	1591	2283	SO:0001819	synonymous_variant	342931	exon3			CGAGCCCTGGCGT		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.747C>A	19.37:g.56274424C>A			234	0	0		153	0.08	13	NM_001145014	2	0.00	0		Silent	SNP	ENST00000434937.2	37	CCDS46201.1																																																																																					0.463	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000384184.1		XM_292796	
RFPL4A	342931	bcgsc.ca	37	19	56274460	56274460	+	Silent	SNP	A	A	G	rs200071964	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:56274460A>G	ENST00000434937.2	+	3	954	c.783A>G	c.(781-783)caA>caG	p.Q261Q		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	261	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GTGGAAGTCAAGATGATCAGA	0.428																																					p.Q261Q													.	RFPL4A	8		0			c.A783G												19.0	22.0	21.0					19																	56274460		691	1590	2281	SO:0001819	synonymous_variant	342931	exon3			AAGTCAAGATGAT		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.783A>G	19.37:g.56274460A>G			206	0.0145631068	3		143	0.07	10	NM_001145014	0		0		Silent	SNP	ENST00000434937.2	37	CCDS46201.1																																																																																					0.428	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000384184.1		XM_292796	
ZNF417	147687	bcgsc.ca;mdanderson.org	37	19	58421141	58421141	+	Missense_Mutation	SNP	G	G	A	rs142466487	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr19:58421141G>A	ENST00000312026.5	-	3	669	c.505C>T	c.(505-507)Cca>Tca	p.P169S	ZNF417_ENST00000536263.1_5'UTR|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000595559.1_Missense_Mutation_p.P168S	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		AAGACAAATGGCTCCTGTGAC	0.473													g|||	182	0.0363419	0.0817	0.0115	5008	,	,		20063	0.0526		0.0099	False		,,,				2504	0.0031				p.P169S													.	ZNF417	44		0			c.C505T							G	SER/PRO	224,3528		36,152,1688	36.0	37.0	37.0		505	-1.9	0.0	19	dbSNP_134	37	57,7957		1,55,3951	no	missense	ZNF417	NM_152475.2	74	37,207,5639	AA,AG,GG		0.7113,5.9701,2.3882	benign	169/576	58421141	281,11485	1876	4007	5883	SO:0001583	missense	147687	exon3			CAAATGGCTCCTG	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.505C>T	19.37:g.58421141G>A	ENSP00000311319:p.Pro169Ser		598	0	0		498	0.04	22	NM_152475	11	0.00	0	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	.	.	.	.	.	.	.	.	.	.	.	2.211	-0.380617	0.05000	0.059701	0.007113	ENSG00000173480	ENST00000312026	T	0.05855	3.38	1.86	-1.91	0.07641	.	.	.	.	.	T	0.00440	0.0014	N	0.21448	0.665	0.25112	N	0.990707	B;B	0.21520	0.057;0.009	B;B	0.20577	0.03;0.002	T	0.42916	-0.9423	9	0.49607	T	0.09	.	3.0609	0.06199	0.2792:0.0:0.5124:0.2083	.	169;169	F5H0M9;Q8TAU3	.;ZN417_HUMAN	S	169	ENSP00000311319:P169S	ENSP00000311319:P169S	P	-	1	0	ZNF417	63112953	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.687000	0.05156	-0.394000	0.07727	-0.708000	0.03648	CCA			0.473	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000466860.1		NM_152475	
DCDC2C	728597	bcgsc.ca	37	2	3800383	3800383	+	Silent	SNP	C	C	T	rs357969	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:3800383C>T	ENST00000399143.3	+	2	72	c.72C>T	c.(70-72)ggC>ggT	p.G24G	DCDC2C_ENST00000537457.1_Intron			A8MYV0	DCD2C_HUMAN	doublecortin domain containing 2C	192	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				intracellular signal transduction (GO:0035556)					breast(1)	1						ATCTTTTGGGCGACTCAAAGG	0.423													c|||	2569	0.512979	0.1672	0.5865	5008	,	,		15986	0.6756		0.5487	False		,,,				2504	0.7239				.													.	.			0			.																																									SO:0001819	synonymous_variant	728597	.			TTTGGGCGACTCA	AC010907	CCDS74481.1	2p25.3	2010-09-24	2010-09-24		ENSG00000214866	ENSG00000214866			32696	protein-coding gene	gene with protein product			"""doublecortin domain containing 2C pseudogene"""				Standard	NM_001287444		Approved			A8MYV0	OTTHUMG00000151490	ENST00000399143.3:c.72C>T	2.37:g.3800383C>T			276	0.0108695652	3		272	0.03	9	.	0		0		Silent	SNP	ENST00000399143.3	37																																																																																						0.423	DCDC2C-201	KNOWN	basic	protein_coding	protein_coding				XM_001715903	
PDIA6	10130	bcgsc.ca;mdanderson.org	37	2	10959407	10959407	+	Missense_Mutation	SNP	A	A	C	rs72779451	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:10959407A>C	ENST00000404371.2	-	3	505	c.168T>G	c.(166-168)aaT>aaG	p.N56K	PDIA6_ENST00000404824.2_Missense_Mutation_p.N52K|PDIA6_ENST00000381611.4_Missense_Mutation_p.N9K	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	0	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.	Contributes to redox potential value. {ECO:0000250}.			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		TACCGGGTGCATTAGCCATGG	0.488													A|||	398	0.0794728	0.0068	0.1268	5008	,	,		19349	0.0585		0.1879	False		,,,				2504	0.0542				.	GBM(73;509 1219 34219 41343 41551)												.	.			0			.																																									SO:0001583	missense	10130	.			GGGTGCATTAGCC	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.168T>G	2.37:g.10959407A>C	ENSP00000385385:p.Asn56Lys		92	0	0		116	0.08	9	.	0		0	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Missense_Mutation	SNP	ENST00000404371.2	37		219	0.10027472527472528	9	0.018292682926829267	36	0.09944751381215469	42	0.07342657342657342	132	0.1741424802110818	A	0.012	-1.674955	0.00751	.	.	ENSG00000143870	ENST00000404371;ENST00000404824;ENST00000381611;ENST00000458536	T;T;T	0.04083	3.71;3.72;3.75	0.94	-1.88	0.07713	.	12.101500	0.00954	N	0.003015	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.43637	-0.9379	8	0.07482	T	0.82	.	3.9079	0.09190	0.5504:0.1958:0.2538:0.0	.	52;56	B5MCQ5;Q15084-2	.;.	K	56;52;9;9	ENSP00000385385:N56K;ENSP00000384459:N52K;ENSP00000371024:N9K	ENSP00000371024:N9K	N	-	3	2	PDIA6	10876858	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.919000	0.01572	-2.629000	0.00435	-1.489000	0.00976	AAT			0.488	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000323575.2		NM_005742	
PDIA6	10130	bcgsc.ca	37	2	10959461	10959461	+	Silent	SNP	G	G	T	rs72779452	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:10959461G>T	ENST00000404371.2	-	3	451	c.114C>A	c.(112-114)gcC>gcA	p.A38A	PDIA6_ENST00000404824.2_Silent_p.A34A|PDIA6_ENST00000381611.4_5'UTR	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	0	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		ATAGGGAGTGGGCAGGAGAAG	0.502													g|||	398	0.0794728	0.0068	0.1268	5008	,	,		19826	0.0585		0.1879	False		,,,				2504	0.0542				.	GBM(73;509 1219 34219 41343 41551)												.	.			0			.																																									SO:0001819	synonymous_variant	10130	.			GGAGTGGGCAGGA	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.114C>A	2.37:g.10959461G>T			83	0	0		98	0.07	7	.	0		0	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000404371.2	37																																																																																						0.502	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000323575.2		NM_005742	
ZFYVE9P2	100420972	bcgsc.ca	37	2	17466075	17466075	+	IGR	SNP	A	A	G	rs10208884	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:17466075A>G								RN7SKP168 (161668 upstream) : RAD51AP2 (225775 downstream)																							TCTGGACAGCACCTTGGTGCC	0.507													G|||	3197	0.638379	0.9486	0.5836	5008	,	,		18515	0.124		0.7435	False		,,,				2504	0.68				.													.	.			0			.																																									SO:0001628	intergenic_variant	100420972	.			GACAGCACCTTGG																													2.37:g.17466075A>G			72	0.0138888889	1		65	0.15	10	.	0		0		RNA	SNP		37																																																																																					0	0.507										
TDRD15	100129278	bcgsc.ca	37	2	21360583	21360583	+	Missense_Mutation	SNP	A	A	G	rs312966	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:21360583A>G	ENST00000405799.1	+	4	574	c.244A>G	c.(244-246)Atg>Gtg	p.M82V				B5MCY1	TDR15_HUMAN	tudor domain containing 15	82	Tudor 1. {ECO:0000255|PROSITE- ProRule:PRU00211}.						hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)										AGGAAGAGTCATGGAAAAGAA	0.383													G|||	2581	0.515375	0.4047	0.4524	5008	,	,		17902	0.7391		0.3668	False		,,,				2504	0.6319				.													.	.			0			.																																									SO:0001583	missense	0	.			AGAGTCATGGAAA			2p24.1	2013-01-23	2013-01-23	2013-01-23	ENSG00000218819	ENSG00000218819		"""Tudor domain containing"""	45037	protein-coding gene	gene with protein product							Standard	XR_425376		Approved			B5MCY1	OTTHUMG00000151795	ENST00000405799.1:c.244A>G	2.37:g.21360583A>G	ENSP00000384376:p.Met82Val		126	0.0079365079	1		122	0.16	19	.	0		0		Missense_Mutation	SNP	ENST00000405799.1	37		1041	0.4766483516483517	191	0.3882113821138211	148	0.4088397790055249	422	0.7377622377622378	280	0.36939313984168864	G	0.006	-2.106441	0.00356	.	.	ENSG00000218819	ENST00000405799	T	0.07908	3.15	5.39	0.00659	0.14068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29822	-0.9999	5	0.08599	T	0.76	-12.4799	0.3815	0.00395	0.2797:0.2181:0.2875:0.2146	rs312966;rs591760;rs17399748;rs56889575;rs312966	.	.	.	V	82	ENSP00000384376:M82V	ENSP00000384376:M82V	M	+	1	0	AC010872.2	21214088	0.000000	0.05858	0.340000	0.25575	0.616000	0.37450	-0.195000	0.09546	-0.668000	0.05296	-0.262000	0.10625	ATG			0.383	TDRD15-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000323948.1			
AC109829.1	0	bcgsc.ca	37	2	27789861	27789861	+	Missense_Mutation	SNP	T	T	A	rs965813	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:27789861T>A	ENST00000447166.1	+	5	675	c.634T>A	c.(634-636)Ttc>Atc	p.F212I																								ATCCTCTGTGTTCAGGAACCA	0.438													T|||	1263	0.252196	0.2163	0.1326	5008	,	,		18406	0.3383		0.2167	False		,,,				2504	0.3333				.													.	.			0			.																																									SO:0001583	missense	0	.			TCTGTGTTCAGGA																												ENST00000447166.1:c.634T>A	2.37:g.27789861T>A	ENSP00000403181:p.Phe212Ile		261	0	0		220	0.05	10	.	1	0.00	0		Missense_Mutation	SNP	ENST00000447166.1	37		502	0.22985347985347984	135	0.27439024390243905	48	0.13259668508287292	168	0.2937062937062937	151	0.19920844327176782	T	3.707	-0.060284	0.07317	.	.	ENSG00000233438	ENST00000447166	.	.	.	5.48	-5.85	0.02311	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.38714	-0.9648	4	0.87932	D	0	.	0.7679	0.01018	0.1487:0.2439:0.2266:0.3808	rs965813;rs965813	.	.	.	I	212	.	ENSP00000403181:F212I	F	+	1	0	AC109829.1	27643365	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-0.802000	0.04545	-0.473000	0.06871	0.529000	0.55759	TTC			0.438	AC109829.1-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000324535.2			
Unknown	0	bcgsc.ca	37	2	43053772	43053772	+	IGR	SNP	C	C	T	rs13013413	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:43053772C>T								HAAO (34040 upstream) : AC016735.1 (174722 downstream)																							GTCCTCTCTACGTGGAACATT	0.403													C|||	590	0.117812	0.0454	0.1196	5008	,	,		21347	0.1776		0.17	False		,,,				2504	0.0992				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTCTACGTGGAA																													2.37:g.43053772C>T			83	0	0		86	0.17	15	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.403										
LINC01118	388948	bcgsc.ca;mdanderson.org	37	2	47045321	47045321	+	Missense_Mutation	SNP	A	A	G	rs17773492	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:47045321A>G	ENST00000409912.1	+	3	419	c.277A>G	c.(277-279)Aac>Gac	p.N93D	AC016722.1_ENST00000409518.1_Missense_Mutation_p.N31D|AC016722.2_ENST00000422294.1_Intron|AC016722.1_ENST00000479311.1_3'UTR																							TCCTCCAGGGAACTCTTTGAA	0.527													A|||	1151	0.229832	0.0552	0.3602	5008	,	,		19790	0.1478		0.3241	False		,,,				2504	0.3609				.													.	.			0			.																																									SO:0001583	missense	0	.			CCAGGGAACTCTT																												ENST00000409912.1:c.277A>G	2.37:g.47045321A>G	ENSP00000386489:p.Asn93Asp		148	0	0		120	0.08	9	.	0		0		Missense_Mutation	SNP	ENST00000409912.1	37		510	0.23351648351648352	40	0.08130081300813008	126	0.34806629834254144	99	0.17307692307692307	245	0.3232189973614776	A	11.50	1.657725	0.29425	.	.	ENSG00000222005	ENST00000409912;ENST00000409518	.	.	.	4.49	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.31475	-0.9942	4	0.87932	D	0	.	5.821	0.18528	0.7871:0.0:0.2129:0.0	rs17773492;rs17773492	.	.	.	D	93;31	.	ENSP00000387072:N31D	N	+	1	0	AC016722.1	46898825	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	-0.071000	0.11505	0.349000	0.23975	0.459000	0.35465	AAC			0.527	AC016722.1-001	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding		OTTHUMT00000329374.1			
LINC01122	400955	bcgsc.ca	37	2	58688907	58688907	+	lincRNA	SNP	G	G	A	rs2075171	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:58688907G>A	ENST00000452840.1	+	0	127																											TTCCTCCTTCGTGCAGCTGGG	0.507													G|||	827	0.165136	0.0386	0.183	5008	,	,		22101	0.2391		0.2644	False		,,,				2504	0.1452				.													.	.			0			.																																											0	.			TCCTTCGTGCAGC																													2.37:g.58688907G>A			291	0.0034364261	1		237	0.07	16	.	66	0.00	0		RNA	SNP	ENST00000452840.1	37																																																																																						0.507	AC007092.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000327022.1			
ZNF638	27332	ucsc.edu;mdanderson.org	37	2	71654529	71654529	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:71654529G>T	ENST00000409544.1	+	24	6160	c.5530G>T	c.(5530-5532)Gaa>Taa	p.E1844*	ZNF638_ENST00000409407.1_Nonsense_Mutation_p.E784*|ZNF638_ENST00000264447.4_Nonsense_Mutation_p.E1844*|ZNF638_ENST00000355812.3_3'UTR	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1844					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AACCATGATTGAAAGACACTT	0.353																																					p.E1844X													.	ZNF638	179		0			c.G5530T												41.0	42.0	42.0					2																	71654529		2202	4298	6500	SO:0001587	stop_gained	27332	exon24			ATGATTGAAAGAC	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5530G>T	2.37:g.71654529G>T	ENSP00000386433:p.Glu1844*		14	0	0		20	0.20	4	NM_014497	353	0.00	0	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Nonsense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	G	51	17.638755	0.99890	.	.	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	.	.	.	5.17	5.17	0.71159	.	0.084638	0.47093	D	0.000252	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-19.1803	14.0447	0.64698	0.0:0.0:1.0:0.0	.	.	.	.	X	1844;1844;784	.	ENSP00000264447:E1844X	E	+	1	0	ZNF638	71508037	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.134000	0.42102	2.681000	0.91329	0.650000	0.86243	GAA			0.353	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000327431.1		NM_014497	
Unknown	0	bcgsc.ca	37	2	81421951	81421951	+	IGR	SNP	A	A	G	rs13430688	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:81421951A>G								AC084193.1 (324636 upstream) : AC012075.2 (267867 downstream)																							CAGGGACTCCACCAGCGAGGG	0.582													g|||	3898	0.778355	0.857	0.6888	5008	,	,		18839	0.8145		0.6899	False		,,,				2504	0.7894				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACTCCACCAGCG																													2.37:g.81421951A>G			54	0.0185185185	1		53	0.17	9	.	0		0		RNA	SNP		37																																																																																					0	0.582										
Unknown	0	bcgsc.ca	37	2	81422135	81422135	+	IGR	SNP	G	G	T	rs6722134	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:81422135G>T								AC084193.1 (324820 upstream) : AC012075.2 (267683 downstream)																							TCGAAGTAGGGGTTGGCCCTG	0.597													g|||	3897	0.778155	0.857	0.6873	5008	,	,		19709	0.8145		0.6899	False		,,,				2504	0.7894				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTAGGGGTTGGC																													2.37:g.81422135G>T			86	0	0		72	0.17	12	.	0		0		RNA	SNP		37																																																																																					0	0.597										
Unknown	0	bcgsc.ca	37	2	81427036	81427036	+	IGR	SNP	C	C	T	rs1809229	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:81427036C>T								AC084193.1 (329721 upstream) : AC012075.2 (262782 downstream)																							CTAATTTTGACGGCCCGTCTT	0.333													.|||	3869	0.772564	0.8555	0.683	5008	,	,		17256	0.8145		0.6819	False		,,,				2504	0.774				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTGACGGCCCG																													2.37:g.81427036C>T			25	0	0		20	0.20	4	.	0		0		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	2	81427187	81427187	+	IGR	SNP	C	C	T	rs2010447	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:81427187C>T								AC084193.1 (329872 upstream) : AC012075.2 (262631 downstream)																							TTTGTTCATGCCTTTGATTCT	0.353													.|||	3984	0.795527	0.9372	0.6916	5008	,	,		16449	0.8145		0.6829	False		,,,				2504	0.774				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCATGCCTTTGA																													2.37:g.81427187C>T			21	0	0		14	0.29	4	.	0		0		RNA	SNP		37																																																																																					0	0.353										
LOC1720	1720	bcgsc.ca	37	2	83084350	83084350	+	IGR	SNP	A	A	T	rs11126880	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:83084350A>T								AC010105.1 (318515 upstream) : AC010744.1 (665587 downstream)																							GTCTTAAACTATTTGTCACAA	0.333													A|||	90	0.0179712	0.0144	0.0274	5008	,	,		16147	0.003		0.0388	False		,,,				2504	0.0102				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAAACTATTTGTC																													2.37:g.83084350A>T			74	0	0		57	0.14	8	.	0		0		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	2	87365531	87365531	+	IGR	SNP	G	G	A	rs200567153	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:87365531G>A								PLGLB1 (116556 upstream) : MIR4771-2 (56377 downstream)																							GGCATTCTACGTCTGTTTCTA	0.373																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCTACGTCTGTT																													2.37:g.87365531G>A			275	0	0		223	0.06	14	.	0		0		RNA	SNP		37																																																																																					0	0.373										
IGKV3D-15	28875	bcgsc.ca;mdanderson.org	37	2	90154131	90154131	+	RNA	SNP	C	C	T	rs77198710	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:90154131C>T	ENST00000417279.2	+	0	267									immunoglobulin kappa variable 3D-15 (gene/pseudogene)																		GGTGCATCCACCAGGGCCACT	0.567													-|||	1102	0.220048	0.4788	0.1383	5008	,	,		15542	0.0823		0.164	False		,,,				2504	0.1278				.													.	.			0			.							A		914,2152		161,592,780	8.0	11.0	10.0			-4.0	0.0	2	dbSNP_134	10	819,6587		60,699,2944	no	intergenic				221,1291,3724	TT,TC,CC		11.0586,29.8108,16.5489			90154131	1733,8739	1533	3703	5236			28875	.			CATCCACCAGGGC	X72815		2p11.2	2012-02-08	2008-09-12		ENSG00000224041	ENSG00000224041		"""Immunoglobulins / IGK locus"""	5824	other	immunoglobulin gene			"""immunoglobulin kappa variable 3D-15"""				Standard	NG_000833		Approved				OTTHUMG00000151568		2.37:g.90154131C>T			395	0	0		340	0.06	21	.	184	0.04	7		RNA	SNP	ENST00000417279.2	37																																																																																						0.567	IGKV3D-15-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323143.2		NG_000833	
IGKV3D-15	28875	bcgsc.ca	37	2	90154203	90154203	+	RNA	SNP	G	G	T	rs190666649	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:90154203G>T	ENST00000417279.2	+	0	339									immunoglobulin kappa variable 3D-15 (gene/pseudogene)																		ACCATCAGCAGCCTGCAGTCT	0.502													-|||	913	0.182308	0.4735	0.0908	5008	,	,		16475	0.0744		0.0944	False		,,,				2504	0.0552				.													.	.			0			.							G		1305,1849		315,675,587	11.0	13.0	12.0			-1.3	0.0	2	dbSNP_134	12	685,6241		53,579,2831	no	intergenic				368,1254,3418	TT,TG,GG		9.8903,41.376,19.7421			90154203	1990,8090	1577	3463	5040			28875	.			TCAGCAGCCTGCA	X72815		2p11.2	2012-02-08	2008-09-12		ENSG00000224041	ENSG00000224041		"""Immunoglobulins / IGK locus"""	5824	other	immunoglobulin gene			"""immunoglobulin kappa variable 3D-15"""				Standard	NG_000833		Approved				OTTHUMG00000151568		2.37:g.90154203G>T			571	0	0		517	0.04	22	.	191	0.00	0		RNA	SNP	ENST00000417279.2	37																																																																																						0.502	IGKV3D-15-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323143.2		NG_000833	
IGKV1D-13	28902	bcgsc.ca	37	2	90193417	90193417	+	RNA	SNP	A	A	G	rs1724244	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:90193417A>G	ENST00000390275.2	+	0	524									immunoglobulin kappa variable 1D-13																		CAGTTTAATAATTACCCTCAC	0.493																																					.													.	.			0			.												30.0	25.0	27.0					2																	90193417		1791	4044	5835			28902	.			TTAATAATTACCC	X17262		2p11.2	2014-05-06			ENSG00000211630	ENSG00000276566		"""Immunoglobulins / IGK locus"""	5747	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000188271		2.37:g.90193417A>G			412	0.0024271845	1		342	0.05	16	.	0		0		RNA	SNP	ENST00000390275.2	37																																																																																						0.493	IGKV1D-13-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323146.2		NG_000833	
IGKV1D-42	28892	bcgsc.ca	37	2	90229260	90229260	+	RNA	SNP	T	T	C	rs842173	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:90229260T>C	ENST00000390278.2	+	0	100									immunoglobulin kappa variable 1D-42 (non-functional)																		ATCCAGATGATCCAGTCTCCA	0.438													C|||	1180	0.235623	0.5325	0.1455	5008	,	,		18968	0.0843		0.164	False		,,,				2504	0.1278				.													.	.			0			.							C		1880,1912		524,832,540	119.0	124.0	123.0			1.3	0.0	2	dbSNP_86	123	1340,6914		140,1060,2927	no	intergenic				664,1892,3467	CC,CT,TT		16.2346,49.5781,26.7309			90229260	3220,8826	1896	4127	6023			28892	.			AGATGATCCAGTC	X72816		2p11.2	2012-02-08	2008-09-09		ENSG00000211633	ENSG00000211633		"""Immunoglobulins / IGK locus"""	5757	other	immunoglobulin gene			"""immunoglobulin kappa variable 1D-42"""				Standard	NG_000833		Approved				OTTHUMG00000151573		2.37:g.90229260T>C			147	0	0		122	0.06	7	.	0		0		RNA	SNP	ENST00000390278.2	37																																																																																						0.438	IGKV1D-42-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323148.1		NG_000833	
IGKV1D-8	28904	bcgsc.ca	37	2	90259965	90259965	+	RNA	SNP	T	T	C	rs842156	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:90259965T>C	ENST00000471857.1	+	0	249									immunoglobulin kappa variable 1D-8																		GCCAGATGTGTCATCTGGATG	0.443													A|||	1009	0.201478	0.5363	0.0994	5008	,	,		18706	0.0744		0.0994	False		,,,				2504	0.0573				.													.	.			0			.							C		1877,1983		517,843,570	96.0	98.0	97.0			-3.5	0.0	2	dbSNP_86	97	796,7456		63,670,3393	no	intergenic				580,1513,3963	CC,CT,TT		9.6461,48.6269,22.069			90259965	2673,9439	1930	4126	6056			28904	.			GATGTGTCATCTG	Z00008		2p11.2	2012-02-08			ENSG00000239819	ENSG00000239819		"""Immunoglobulins / IGK locus"""	5759	other	immunoglobulin gene							Standard	NG_000833		Approved				OTTHUMG00000151570		2.37:g.90259965T>C			282	0.0070921986	2		212	0.09	19	.	1	0.00	0		RNA	SNP	ENST00000471857.1	37																																																																																						0.443	IGKV1D-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323145.2		NG_000833	
Unknown	0	bcgsc.ca	37	2	91800282	91800282	+	IGR	SNP	A	A	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:91800282A>G								RP11-575H3.1 (31362 upstream) : AC027612.6 (4903 downstream)																							CCTATGGAAGAACATCGGGCG	0.557																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGAAGAACATCG																													2.37:g.91800282A>G			283	0	0		281	0.03	8	.	0		0		RNA	SNP		37																																																																																					0	0.557										
TRIM51JP	643126	bcgsc.ca	37	2	96241051	96241051	+	IGR	SNP	G	G	A	rs1974909	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:96241051G>A								RP11-440D17.4 (36834 upstream) : TRIM43 (16714 downstream)																							GGCTGCTGAGGAACACCGGGT	0.493													.|||	700	0.139776	0.23	0.1311	5008	,	,		20253	0.1369		0.0895	False		,,,				2504	0.0787				.													.	.			0			.																																									SO:0001628	intergenic_variant	643126	.			GCTGAGGAACACC																													2.37:g.96241051G>A			150	0	0		95	0.07	7	.	0		0		RNA	SNP		37																																																																																					0	0.493										
IL1RL1	9173	ucsc.edu;bcgsc.ca	37	2	102968211	102968212	+	Missense_Mutation	DNP	CA	CA	AG	rs386648697|rs10192036|rs10204137	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:102968211_102968212CA>AG	ENST00000233954.1	+	11	1772_1773	c.1501_1502CA>AG	c.(1501-1503)CAg>AGg	p.Q501R		NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	501	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.		Q -> K (in dbSNP:rs10192036).|Q -> R (in dbSNP:rs10204137).		immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						GGACTCCCTCCAGCATCTTATG	0.52																																					p.Q501R													.	IL1RL1	114		0			c.A1502G																																									SO:0001583	missense	9173	exon11			TCCCTCCAGCATC	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	Exception_encountered	2.37:g.102968211_102968212delinsAG	ENSP00000233954:p.Gln501Arg		184	0.0054347826	1		144	0.13	18	NM_016232	0		0	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	DNP	ENST00000233954.1	37	CCDS2057.1																																																																																					0.520	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253296.1		NM_016232	
Unknown	0	bcgsc.ca	37	2	124520286	124520286	+	IGR	SNP	G	G	C	rs12997146	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:124520286G>C								AC092646.3 (80495 upstream) : RN7SKP102 (106546 downstream)																							ACTTAAACAAGCCATCTATCC	0.333													G|||	594	0.11861	0.0242	0.147	5008	,	,		21161	0.0238		0.2922	False		,,,				2504	0.1452				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAACAAGCCATCT																													2.37:g.124520286G>C			37	0	0		34	0.15	5	.	0		0		RNA	SNP		37																																																																																					0	0.333										
ISCA1P6	100130549	bcgsc.ca	37	2	129276720	129276720	+	IGR	SNP	T	T	C	rs841094	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:129276720T>C								RNA5SP103 (73948 upstream) : AC012451.1 (61344 downstream)																							GCTCACAGCCTGGACAGTTGC	0.602													C|||	1912	0.381789	0.8782	0.2954	5008	,	,		15608	0.0942		0.2366	False		,,,				2504	0.2178				.													.	.			0			.																																									SO:0001628	intergenic_variant	100130549	.			ACAGCCTGGACAG																													2.37:g.129276720T>C			196	0	0		217	0.09	20	.	0		0		RNA	SNP		37																																																																																					0	0.602										
LOC401010	401010	bcgsc.ca	37	2	132201466	132201466	+	IGR	SNP	G	G	A	rs66493058|rs112041013	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132201466G>A								AC073869.19 (34844 upstream) : RP11-109E12.1 (17927 downstream)																							CTTGAGGACGGGGCCAAGGAA	0.577													.|||	85	0.0169728	0.0015	0.0216	5008	,	,		20654	0.0		0.0577	False		,,,				2504	0.0102				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGACGGGGCCAA																													2.37:g.132201466G>A			242	0	0		179	0.06	11	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.577										
LOC401010	401010	bcgsc.ca	37	2	132201468	132201468	+	IGR	SNP	G	G	A	rs66493058|rs4522649	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132201468G>A								AC073869.19 (34846 upstream) : RP11-109E12.1 (17925 downstream)																							TGAGGACGGGGCCAAGGAAAG	0.577													.|||	1761	0.351637	0.084	0.5086	5008	,	,		20647	0.7579		0.2286	False		,,,				2504	0.3098				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACGGGGCCAAGG																													2.37:g.132201468G>A			247	0	0		179	0.07	13	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.577										
LOC401010	401010	bcgsc.ca	37	2	132201582	132201582	+	IGR	SNP	A	A	G	rs1806886	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132201582A>G								AC073869.19 (34960 upstream) : RP11-109E12.1 (17811 downstream)																							TAAGCAGCATACGGCACTGCT	0.602													.|||	2073	0.413938	0.2958	0.5346	5008	,	,		21057	0.7589		0.2366	False		,,,				2504	0.3149				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGCATACGGCAC																													2.37:g.132201582A>G			116	0	0		101	0.09	9	.	16	1.00	16		RNA	SNP		37																																																																																					0	0.602										
LOC401010	401010	bcgsc.ca	37	2	132201736	132201736	+	IGR	SNP	C	C	G	rs2076798	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132201736C>G								AC073869.19 (35114 upstream) : RP11-109E12.1 (17657 downstream)																							CCCCCAGAGCCGGCTGCTGGA	0.592													.|||	1941	0.38758	0.2035	0.5259	5008	,	,		18957	0.7589		0.2326	False		,,,				2504	0.3149				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGAGCCGGCTGC																													2.37:g.132201736C>G			58	0	0		59	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.592										
LOC150776	150776	bcgsc.ca	37	2	132257830	132257830	+	RNA	SNP	C	C	T	rs13035779	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132257830C>T	ENST00000438378.2	+	0	553					NR_026922.1																						GCAGCCTAGACGGTGTCCTCG	0.567													.|||	1676	0.334665	0.1346	0.4265	5008	,	,		18990	0.6806		0.2197	False		,,,				2504	0.3016				.													.	.			0			.																																											0	.			CCTAGACGGTGTC																													2.37:g.132257830C>T			220	0	0		192	0.07	13	.	13	0.00	0		RNA	SNP	ENST00000438378.2	37																																																																																						0.567	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331819.7			
LOC150776	150776	bcgsc.ca	37	2	132258593	132258593	+	RNA	SNP	A	A	G	rs13415770	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:132258593A>G	ENST00000438378.2	+	0	777					NR_026922.1																						CTGTACCACAACAAGGTCCAG	0.617													.|||	1503	0.30012	0.0189	0.4092	5008	,	,		19153	0.6796		0.2157	False		,,,				2504	0.2986				.													.	.			0			.																																											0	.			ACCACAACAAGGT																													2.37:g.132258593A>G			164	0	0		145	0.04	6	.	31	0.00	0		RNA	SNP	ENST00000438378.2	37																																																																																						0.617	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331819.7			
YWHAEP5	440917	bcgsc.ca	37	2	139045855	139045855	+	IGR	SNP	C	C	T	rs35998722	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:139045855C>T								AC069394.1 (182380 upstream) : AC097721.2 (129998 downstream)																							AAGACCTAAGCGAATAGGATG	0.438													C|||	1236	0.246805	0.2542	0.2896	5008	,	,		19651	0.4851		0.1163	False		,,,				2504	0.0951				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTAAGCGAATAG																													2.37:g.139045855C>T			136	0	0		118	0.07	8	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.438										
YWHAEP5	440917	bcgsc.ca	37	2	139045987	139045987	+	IGR	SNP	C	C	T	rs13033503	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:139045987C>T								AC069394.1 (182512 upstream) : AC097721.2 (129866 downstream)																							GTGGTAGTACCATTTCGTTTT	0.423													C|||	1236	0.246805	0.2542	0.2896	5008	,	,		19168	0.4851		0.1163	False		,,,				2504	0.0951				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAGTACCATTTCG																													2.37:g.139045987C>T			186	0	0		138	0.05	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.423										
CTAGE14P	401018	bcgsc.ca	37	2	168571044	168571044	+	IGR	SNP	T	T	C	rs7577934	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:168571044T>C								RNU7-148P (82993 upstream) : AC016723.4 (100239 downstream)																							CTGCCAAATGTTGTATTTGAA	0.393													C|||	1422	0.283946	0.6021	0.379	5008	,	,		21352	0.2659		0.0378	False		,,,				2504	0.0583				.													.	.			0			.																																									SO:0001628	intergenic_variant	401018	.			CAAATGTTGTATT																													2.37:g.168571044T>C			122	0	0		121	0.12	14	.	0		0		RNA	SNP		37																																																																																					0	0.393										
CTAGE14P	401018	bcgsc.ca	37	2	168571488	168571488	+	IGR	SNP	A	A	T	rs34125069	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:168571488A>T								RNU7-148P (83437 upstream) : AC016723.4 (99795 downstream)																							GACTGCAAAGATGCTTGTTGA	0.318													A|||	1124	0.224441	0.3986	0.3473	5008	,	,		20200	0.2599		0.0378	False		,,,				2504	0.0573				.													.	.			0			.																																									SO:0001628	intergenic_variant	401018	.			GCAAAGATGCTTG																													2.37:g.168571488A>T			78	0	0		58	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.318										
LRP2	4036	bcgsc.ca;mdanderson.org	37	2	170150695	170150695	+	Silent	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:170150695G>A	ENST00000263816.3	-	6	900	c.615C>T	c.(613-615)gaC>gaT	p.D205D	LRP2_ENST00000443831.1_Silent_p.D205D	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	205	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GGCAATCATTGTCATGGTCAC	0.438																																					p.D205D													.	LRP2	751		0			c.C615T												173.0	142.0	153.0					2																	170150695		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon6			ATCATTGTCATGG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.615C>T	2.37:g.170150695G>A			612	0.0016339869	1		476	0.08	40	NM_004525	1	1.00	1	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																					0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255231.2		NM_004525	
UBR3	130507	hgsc.bcm.edu	37	2	170783231	170783231	+	Nonsense_Mutation	SNP	T	T	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:170783231T>G	ENST00000272793.5	+	15	2231	c.2181T>G	c.(2179-2181)taT>taG	p.Y727*	UBR3_ENST00000418381.1_Nonsense_Mutation_p.Y727*			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	727					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						ACCCAGATTATTTTATTTCAT	0.264																																					p.Y727X													.	.			0			c.T2181G												108.0	95.0	99.0					2																	170783231		692	1591	2283	SO:0001587	stop_gained	130507	exon15			AGATTATTTTATT	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.2181T>G	2.37:g.170783231T>G	ENSP00000272793:p.Tyr727*		205	0	0		190	0.05	10	NM_172070	15	0.07	1	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Nonsense_Mutation	SNP	ENST00000272793.5	37		.	.	.	.	.	.	.	.	.	.	T	38	6.906983	0.97924	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	.	.	.	5.45	0.402	0.16344	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.7288	0.08485	0.151:0.2519:0.0:0.5971	.	.	.	.	X	727	.	ENSP00000272793:Y727X	Y	+	3	2	UBR3	170491477	1.000000	0.71417	0.983000	0.44433	0.993000	0.82548	1.063000	0.30567	-0.151000	0.11176	0.455000	0.32223	TAT			0.264	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000255290.2		NM_172070	
Unknown	0	bcgsc.ca	37	2	194141586	194141586	+	IGR	SNP	A	A	T	rs11675750	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:194141586A>T								PCGEM1 (499961 upstream) : RP11-764E7.1 (621504 downstream)																							TCAGAGGGTTATCCACCAGGC	0.592													A|||	634	0.126597	0.0764	0.0951	5008	,	,		14627	0.128		0.172	False		,,,				2504	0.1687				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGGTTATCCACC																													2.37:g.194141586A>T			182	0	0		137	0.07	9	.	0		0		RNA	SNP		37																																																																																					0	0.592										
LOC101927641	101927641	bcgsc.ca	37	2	200525076	200525076	+	lincRNA	SNP	A	A	G	rs77443884	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:200525076A>G	ENST00000439734.1	+	0	4574																											CACTGACATCAAGGGCTTTGG	0.587													A|||	445	0.0888578	0.0098	0.0893	5008	,	,		18906	0.0377		0.1561	False		,,,				2504	0.1789				.													.	.			0			.																																											729399	.			GACATCAAGGGCT																													2.37:g.200525076A>G			75	0	0		52	0.12	6	.	0		0		RNA	SNP	ENST00000439734.1	37																																																																																						0.587	AC093590.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000335491.2			
KIAA2012	100652824	ucsc.edu;bcgsc.ca;mdanderson.org	37	2	202974360	202974360	+	Missense_Mutation	SNP	T	T	G	rs12615065	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:202974360T>G	ENST00000541917.1	+	10	1977	c.1604T>G	c.(1603-1605)gTg>gGg	p.V535G	AC079354.1_ENST00000295844.3_Missense_Mutation_p.V591G|AC079354.1_ENST00000409515.3_3'UTR																							CCTCACGATGTGGCCCCACCA	0.493													T|||	641	0.127995	0.0325	0.1037	5008	,	,		18400	0.1776		0.1938	False		,,,				2504	0.1554				.													.	.			0			.																																									SO:0001583	missense	0	.			ACGATGTGGCCCC																												ENST00000541917.1:c.1604T>G	2.37:g.202974360T>G	ENSP00000437957:p.Val535Gly		91	0	0		80	0.15	12	.	9	0.00	0		Missense_Mutation	SNP	ENST00000541917.1	37		328	0.15018315018315018	28	0.056910569105691054	50	0.13812154696132597	105	0.18356643356643357	145	0.19129287598944592	T	8.312	0.822381	0.16678	.	.	ENSG00000182329	ENST00000541917;ENST00000295844;ENST00000498697	.	.	.	5.2	-6.29	0.02013	.	2.719930	0.01324	N	0.011020	T	0.00039	0.0001	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.0	B;B	0.08055	0.001;0.003	T	0.11155	-1.0599	8	0.14656	T	0.56	.	4.6908	0.12780	0.1081:0.4441:0.1103:0.3375	rs12615065;rs60754455;rs12615065	500;591	B4DIH8;E7EP55	.;.	G	535;591;120	.	ENSP00000295844:V591G	V	+	2	0	AC079354.1	202682605	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.604000	0.02076	-1.117000	0.02965	-1.139000	0.01908	GTG			0.493	AC079354.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
KIAA2012	100652824	bcgsc.ca	37	2	203003085	203003085	+	Intron	SNP	T	T	C	rs16838883	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:203003085T>C	ENST00000409515.3	+	14	2244				AC079354.1_ENST00000295844.3_Intron|AC079354.1_ENST00000541917.1_Intron																							GTGTGTATGGTATATATAAAA	0.358													T|||	2029	0.405152	0.3669	0.4035	5008	,	,		18697	0.5833		0.3419	False		,,,				2504	0.3395				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			GTATGGTATATAT																												ENST00000409515.3:c.2245-70T>C	2.37:g.203003085T>C			100	0	0		71	0.10	7	.	0		0		RNA	SNP	ENST00000409515.3	37																																																																																						0.358	AC079354.1-001	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000336161.2			
DAZAP2P1	645805	bcgsc.ca	37	2	203066419	203066419	+	IGR	SNP	C	C	T	rs10931992	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:203066419C>T								AC079354.5 (22305 upstream) : SUMO1 (4483 downstream)																							TCCAGGAAAGCGGCCGACATG	0.557													C|||	1432	0.285942	0.1271	0.2651	5008	,	,		19759	0.5704		0.2744	False		,,,				2504	0.2342				.													.	.			0			.																																									SO:0001628	intergenic_variant	645805	.			GGAAAGCGGCCGA																													2.37:g.203066419C>T			80	0	0		60	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.557										
Unknown	0	bcgsc.ca	37	2	207275255	207275256	+	IGR	INS	-	-	CTGGTCTTG	rs59366011|rs368877978|rs57664845|rs377108276		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:207275255_207275256insCTGGTCTTG								AC017081.1 (54412 upstream) : ADAM23 (33006 downstream)																							CACAGACCACCACCTTGAACCT	0.515																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACCACCACCTTG																													2.37:g.207275255_207275256insCTGGTCTTG			120	0	0		84	0.04	3	.	0		0		RNA	INS		37																																																																																					0	0.515										
CRYGEP	200575	bcgsc.ca	37	2	208977135	208977135	+	RNA	SNP	A	A	G	rs35960349	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:208977135A>G	ENST00000440809.1	-	0	97									crystallin, gamma E, pseudogene																		GTCCACGCGCACCGAGTTGCA	0.657													A|||	1140	0.227636	0.0976	0.232	5008	,	,		13910	0.1518		0.3618	False		,,,				2504	0.3405				.													.	.			0			.																																											200575	.			ACGCGCACCGAGT	K03007		2q33.3	2012-02-29	2009-12-02	2009-12-02	ENSG00000229150	ENSG00000229150			2412	pseudogene	pseudogene			"""crystallin, gamma E pseudogene 1"""	CRYG5, CCL, CRYGEP1		8004095	Standard	NG_002762		Approved	G2			OTTHUMG00000154792		2.37:g.208977135A>G			68	0	0		63	0.11	7	.	1	0.00	0		RNA	SNP	ENST00000440809.1	37																																																																																						0.657	CRYGEP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000337069.1			
CRYGB	1419	bcgsc.ca	37	2	209010891	209010891	+	5'UTR	SNP	G	G	A	rs2289917	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:209010891G>A	ENST00000260988.4	-	0	1					NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B						lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		GTGGGACTGCGGGAACGTCAC	0.522													G|||	1138	0.227236	0.1036	0.2118	5008	,	,		20854	0.1448		0.3986	False		,,,				2504	0.3139				.													.	.			0			.							G		704,3702	294.4+/-283.1	59,586,1558	92.0	71.0	78.0			3.3	0.3	2	dbSNP_100	78	3428,5172	504.7+/-376.2	687,2054,1559	no	near-gene-5				746,2640,3117	AA,AG,GG		39.8605,15.9782,31.77			209010891	4132,8874	2203	4300	6503	SO:0001623	5_prime_UTR_variant	1419	.			GACTGCGGGAACG		CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"""crystallin, gamma 1-2"""	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.-47C>T	2.37:g.209010891G>A			114	0	0		124	0.15	19	.	0		0	Q17RB5|Q53ST2	Missense_Mutation	SNP	ENST00000260988.4	37	CCDS2380.1																																																																																					0.522	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256473.2		NM_005210	
CCDC108	255101	hgsc.bcm.edu	37	2	219870199	219870199	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:219870199G>T	ENST00000341552.5	-	32	5091	c.5008C>A	c.(5008-5010)Cag>Aag	p.Q1670K	CCDC108_ENST00000453220.1_Missense_Mutation_p.Q1670K|CCDC108_ENST00000441968.1_Missense_Mutation_p.Q1670K|AC097468.4_ENST00000441450.1_RNA	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1670						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCTTCTTCTGCTTGGAAACA	0.547																																					p.Q1670K													CCDC108,NS,carcinoma,+2,1	CCDC108	2	1	0			c.C5008A												132.0	127.0	129.0					2																	219870199		2202	4300	6502	SO:0001583	missense	255101	exon32			TCTTCTGCTTGGA	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.5008C>A	2.37:g.219870199G>T	ENSP00000340776:p.Gln1670Lys		140	0	0		120	0.04	5	NM_194302	0		0	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	G	9.159	1.018325	0.19355	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.04970	3.52;3.52;3.52	4.31	3.42	0.39159	.	0.000000	0.42420	D	0.000719	T	0.09158	0.0226	M	0.66939	2.045	0.80722	D	1	B	0.30236	0.274	B	0.30179	0.112	T	0.05666	-1.0871	10	0.62326	D	0.03	-6.1898	10.1607	0.42849	0.0:0.2203:0.7797:0.0	.	1670	Q6ZU64	CC108_HUMAN	K	1670	ENSP00000340776:Q1670K;ENSP00000413377:Q1670K;ENSP00000409117:Q1670K	ENSP00000340776:Q1670K	Q	-	1	0	CCDC108	219578443	0.953000	0.32496	0.963000	0.40424	0.142000	0.21351	1.707000	0.37888	1.162000	0.42619	0.561000	0.74099	CAG			0.547	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000256598.4		NM_194302	
HSPA9P1	266724	bcgsc.ca	37	2	222828022	222828022	+	IGR	SNP	G	G	T	rs76862842	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:222828022G>T								AC068489.1 (321489 upstream) : PAX3 (236584 downstream)																							ATTTGACATTGATGCCAATGG	0.433													G|||	55	0.0109824	0.0015	0.0173	5008	,	,		20377	0.001		0.0378	False		,,,				2504	0.002				.													.	.			0			.																																									SO:0001628	intergenic_variant	266724	.			GACATTGATGCCA																													2.37:g.222828022G>T			127	0.0078740157	1		117	0.07	8	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.433										
MFF	56947	ucsc.edu;bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	rs3211098|rs3211097|rs386655869	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:228194480_228194481AG>TT	ENST00000353339.3	+	3	460_461	c.19_20AG>TT	c.(19-21)AGt>TTt	p.S7F	MFF_ENST00000337110.7_Intron|MFF_ENST00000409616.1_5'UTR|MFF_ENST00000476924.1_Intron|MFF_ENST00000349901.7_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000409565.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7F	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	7			S -> C (in dbSNP:rs3211097).|S -> I (in dbSNP:rs3211098).		mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)			breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						AGGAACAAGCAGTGACACATCA	0.366																																					p.S7F													.	MFF	48		0			c.G20T																																									SO:0001583	missense	56947	exon3			ACAAGCAGTGACA	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	Exception_encountered	2.37:g.228194480_228194481delinsTT	ENSP00000302037:p.Ser7Phe		327	0.003058104	1		310	0.12	37	NM_020194	17	0.00	0	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Missense_Mutation	DNP	ENST00000353339.3	37	CCDS2465.1																																																																																					0.366	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000256887.2		NM_020194	
SLC16A14	151473	hgsc.bcm.edu;bcgsc.ca	37	2	230924017	230924017	+	Missense_Mutation	SNP	C	C	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:230924017C>A	ENST00000295190.4	-	2	510	c.52G>T	c.(52-54)Gac>Tac	p.D18Y	RNY4P19_ENST00000362530.1_RNA	NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		GTCTTTTTGTCTTTGGGGCCA	0.408																																					p.D18Y													SLC16A14,NS,carcinoma,0,1	SLC16A14	0	1	0			c.G52T												80.0	76.0	77.0					2																	230924017		2203	4300	6503	SO:0001583	missense	151473	exon2			TTTTGTCTTTGGG	BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"""Solute carriers"""	26417	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 14"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 14"""				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.52G>T	2.37:g.230924017C>A	ENSP00000295190:p.Asp18Tyr		256	0	0		204	0.05	10	NM_152527	8	0.00	0	A8KA08|Q53R92|Q96NI7	Missense_Mutation	SNP	ENST00000295190.4	37	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461634	0.26248	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034;ENST00000425822;ENST00000436869	T;T;T	0.09073	3.02;3.02;3.02	5.5	4.61	0.57282	Major facilitator superfamily domain, general substrate transporter (1);	0.860817	0.10169	N	0.707334	T	0.04861	0.0131	N	0.08118	0	0.26007	N	0.982047	P;P	0.44344	0.833;0.612	B;B	0.36766	0.232;0.172	T	0.31308	-0.9948	10	0.62326	D	0.03	.	9.8546	0.41077	0.0:0.8444:0.0:0.1556	.	18;18	E7EMG7;Q7RTX9	.;MOT14_HUMAN	Y	18	ENSP00000295190:D18Y;ENSP00000400352:D18Y;ENSP00000395775:D18Y	ENSP00000295190:D18Y	D	-	1	0	SLC16A14	230632261	0.878000	0.30173	0.460000	0.27093	0.245000	0.25701	2.140000	0.42159	1.529000	0.49120	0.655000	0.94253	GAC			0.408	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256918.2		NM_152527	
SAG	6295	bcgsc.ca;mdanderson.org	37	2	234255547	234255548	+	Missense_Mutation	DNP	GT	GT	AC	rs1046974|rs1046976	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:234255547_234255548GT>AC	ENST00000409110.1	+	16	1437_1438	c.1207_1208GT>AC	c.(1207-1209)GTt>ACt	p.V403T		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	403			V -> A (in dbSNP:rs1046976). {ECO:0000269|PubMed:3164688, ECO:0000269|PubMed:9020843}.|V -> I (in dbSNP:rs1046974).		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CAAGAATGACGTTGATGAGTGA	0.455																																					p.V403T													.	SAG	77		0			c.T1208C																																									SO:0001583	missense	6295	exon16			AATGACGTTGATG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	Exception_encountered	2.37:g.234255547_234255548delinsAC	ENSP00000386444:p.Val403Thr		109	0	0		86	0.08	7	NM_000541	3	0.00	0	A0FDN6|Q53SV3|Q99858	Missense_Mutation	DNP	ENST00000409110.1	37	CCDS46545.1																																																																																					0.455	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000330126.1		NM_000541	
MROH2A	339766	bcgsc.ca	37	2	234708428	234708428	+	Silent	SNP	G	G	A	rs13013882	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:234708428G>A	ENST00000389758.3	+	13	1498	c.1332G>A	c.(1330-1332)gtG>gtA	p.V444V				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	474																	CCCCTCAGGTGAGGATGGCTA	0.582													G|||	3165	0.631989	0.6006	0.549	5008	,	,		19933	0.378		0.8181	False		,,,				2504	0.8037				.													.	.			0			.																																									SO:0001819	synonymous_variant	339766	.			TCAGGTGAGGATG		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.1332G>A	2.37:g.234708428G>A			109	0.0091743119	1		110	0.15	17	.	0		0		Silent	SNP	ENST00000389758.3	37																																																																																						0.582	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
MROH2A	339766	bcgsc.ca;mdanderson.org	37	2	234710831	234710831	+	Silent	SNP	G	G	C	rs10929306	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:234710831G>C	ENST00000389758.3	+	15	1744	c.1578G>C	c.(1576-1578)ctG>ctC	p.L526L				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	556																	GGGTGAGGCTGCTGTGCTACA	0.552													C|||	1678	0.335064	0.5552	0.3256	5008	,	,		18869	0.3601		0.2068	False		,,,				2504	0.1503				.													.	.			0			.																																									SO:0001819	synonymous_variant	339766	.			GAGGCTGCTGTGC		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.1578G>C	2.37:g.234710831G>C			95	0	0		88	0.16	14	.	0		0		Silent	SNP	ENST00000389758.3	37																																																																																						0.552	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
MROH2A	339766	bcgsc.ca	37	2	234716426	234716426	+	Silent	SNP	G	G	A	rs11563241	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:234716426G>A	ENST00000389758.3	+	21	2386	c.2220G>A	c.(2218-2220)acG>acA	p.T740T				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	770																	AGGTAAAAACGGTGCTGAATG	0.602													G|||	1629	0.32528	0.5189	0.3256	5008	,	,		20160	0.3611		0.2048	False		,,,				2504	0.1503				.													.	.			0			.																																									SO:0001819	synonymous_variant	339766	.			AAAAACGGTGCTG		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.2220G>A	2.37:g.234716426G>A			209	0.009569378	2		122	0.06	7	.	0		0		Silent	SNP	ENST00000389758.3	37																																																																																						0.602	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
MROH2A	339766	bcgsc.ca	37	2	234727333	234727333	+	Missense_Mutation	SNP	C	C	G	rs719418	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:234727333C>G	ENST00000389758.3	+	29	3287	c.3121C>G	c.(3121-3123)Cag>Gag	p.Q1041E				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	1071																	CCCTTCCAAGCAGAAGGAGCT	0.572													g|||	1432	0.285942	0.5446	0.17	5008	,	,		20400	0.5089		0.0199	False		,,,				2504	0.0624				.													.	.			0			.																																									SO:0001583	missense	339766	.			TCCAAGCAGAAGG		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.3121C>G	2.37:g.234727333C>G	ENSP00000374408:p.Gln1041Glu		170	0	0		163	0.05	8	.	0		0		Missense_Mutation	SNP	ENST00000389758.3	37		634	0.2902930402930403	260	0.5284552845528455	76	0.20994475138121546	279	0.48776223776223776	19	0.025065963060686015	g	0.004	-2.371226	0.00209	.	.	ENSG00000185038	ENST00000389758	T	0.05319	3.46	4.98	4.1	0.47936	.	.	.	.	.	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	.	.	.	.	.	.	T	0.41840	-0.9486	6	0.02654	T	1	.	7.2396	0.26090	0.0923:0.1702:0.7375:0.0	rs719418;rs719418	.	.	.	E	1041	ENSP00000374408:Q1041E	ENSP00000374408:Q1041E	Q	+	1	0	HEATR7B1	234392072	0.844000	0.29557	0.131000	0.22000	0.150000	0.21749	2.093000	0.41710	0.529000	0.28599	-0.971000	0.02607	CAG			0.572	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
CROCC2	728763	bcgsc.ca	37	2	241865211	241865211	+	Missense_Mutation	SNP	G	G	A	rs56199645	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr2:241865211G>A	ENST00000430980.2	+	2	148	c.148G>A	c.(148-150)Gcg>Acg	p.A50T																								GGCCAATGACGCGCTGGGCCG	0.682													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16913	0.0		0.001	False		,,,				2504	0.002				.													.	.			0			.																																									SO:0001583	missense	0	.			AATGACGCGCTGG																												ENST00000430980.2:c.148G>A	2.37:g.241865211G>A	ENSP00000387851:p.Ala50Thr		218	0	0		181	0.07	12	.	0		0		Missense_Mutation	SNP	ENST00000430980.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	6.125|6.125	0.391209|0.391209	0.11581|0.11581	.|.	.|.	ENSG00000226321|ENSG00000226321	ENST00000430980|ENST00000427156	T|.	0.18960|.	2.18|.	4.3|4.3	-6.85|-6.85	0.01681|0.01681	.|.	.|.	.|.	.|.	.|.	T|T	0.27384|0.27384	0.0672|0.0672	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36261|0.36261	-0.9755|-0.9755	5|3	0.30854|.	T|.	0.27|.	.|.	7.8443|7.8443	0.29417|0.29417	0.6907:0.0:0.1994:0.1098|0.6907:0.0:0.1994:0.1098	rs56199645|rs56199645	.|.	.|.	.|.	T|H	50|141	ENSP00000387851:A50T|.	ENSP00000387851:A50T|.	A|R	+|+	1|2	0|0	AC104809.3|AC104809.3	241513884|241513884	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.002000|0.002000	0.02628|0.02628	-0.604000|-0.604000	0.05667|0.05667	-1.381000|-1.381000	0.02112|0.02112	-1.148000|-1.148000	0.01847|0.01847	GCG|CGC			0.682	AC104809.3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding					
TARDBPP1	643503	bcgsc.ca	37	20	6182755	6182755	+	IGR	SNP	C	C	T	rs3747924	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr20:6182755C>T								FERMT1 (78564 upstream) : AL109618.1 (26685 downstream)																							TAACTGTGGACAGCAGCACCA	0.443													C|||	1183	0.236222	0.4092	0.1326	5008	,	,		20650	0.127		0.1899	False		,,,				2504	0.2362				.													.	.			0			.																																									SO:0001628	intergenic_variant	643503	.			TGTGGACAGCAGC																													20.37:g.6182755C>T			30	0	0		20	0.20	4	.	0		0		RNA	SNP		37																																																																																					0	0.443										
LOC101929413	101929413	broad.mit.edu	37	20	10869748	10869748	+	lincRNA	DEL	T	T	-			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr20:10869748delT	ENST00000448859.1	-	0	1058				RP11-103J8.1_ENST00000605292.1_RNA																							TCtttttttattttttttttt	0.438																																					.													.	.			0			.																																											0	.			TTTTTATTTTTTT																													20.37:g.10869748delT			8	0	0		6	0.33	2	.	0		0		RNA	DEL	ENST00000448859.1	37																																																																																						0.438	RP4-697P8.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000078011.1			
EFCAB8	388795	bcgsc.ca	37	20	31481077	31481077	+	Missense_Mutation	SNP	C	C	T	rs73904069	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr20:31481077C>T	ENST00000400522.4	+	9	950	c.856C>T	c.(856-858)Cgt>Tgt	p.R286C				A8MWE9	EFCB8_HUMAN	EF-hand calcium binding domain 8	0							calcium ion binding (GO:0005509)			endometrium(2)	2						GTTCAACCCCCGTATCCTCCC	0.577													C|||	161	0.0321486	0.1097	0.0159	5008	,	,		18936	0.0		0.004	False		,,,				2504	0.001				.													.	.			0			.							C	CYS/ARG	146,1238		7,132,553	105.0	107.0	107.0		856	-1.5	0.0	20	dbSNP_130	107	10,3172		0,10,1581	no	missense	EFCAB8	XM_003118799.2	180	7,142,2134	TT,TC,CC		0.3143,10.5491,3.4166	probably-damaging	286/1340	31481077	156,4410	692	1591	2283	SO:0001583	missense	388795	.			AACCCCCGTATCC			20q11.21	2013-01-10			ENSG00000215529	ENSG00000215529		"""WD repeat domain containing"", ""EF-hand domain containing"""	34532	protein-coding gene	gene with protein product							Standard	XM_006710086		Approved			A8MWE9	OTTHUMG00000153693	ENST00000400522.4:c.856C>T	20.37:g.31481077C>T	ENSP00000383366:p.Arg286Cys		154	0	0		191	0.04	7	.	0		0		Missense_Mutation	SNP	ENST00000400522.4	37																																																																																						0.577	EFCAB8-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000332144.2		XM_371397	
ANKRD20A18P	391269	bcgsc.ca	37	21	15436681	15436681	+	RNA	SNP	G	G	C	rs11908695	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:15436681G>C	ENST00000428809.1	+	0	177				AP001347.6_ENST00000448463.1_RNA|AP001347.6_ENST00000432621.1_RNA																							GCAGGGGCCAGATGGTCCTGG	0.607													G|||	1620	0.323482	0.2844	0.402	5008	,	,		10771	0.2688		0.3191	False		,,,				2504	0.3814				.													.	.			0			.																																											391269	.			GGGCCAGATGGTC																													21.37:g.15436681G>C			256	0.00390625	1		249	0.10	25	.	4	0.00	0		RNA	SNP	ENST00000428809.1	37																																																																																						0.607	AP001347.6-001	KNOWN	basic	antisense	antisense		OTTHUMT00000157812.1			
PPIAP22	653214	bcgsc.ca	37	21	20230102	20230102	+	IGR	SNP	C	C	T	rs2825212	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:20230102C>T								AL109763.2 (97781 upstream) : AL157359.4 (60149 downstream)																							TAGCCATGGTCAACCCCACCG	0.542													C|||	1384	0.276358	0.0953	0.2334	5008	,	,		17653	0.3581		0.3658	False		,,,				2504	0.3753				.													.	.			0			.																																									SO:0001628	intergenic_variant	653214	.			CATGGTCAACCCC																													21.37:g.20230102C>T			265	0.0113207547	3		271	0.06	15	.	5048	0.00	6		RNA	SNP		37																																																																																					0	0.542										
SLC6A6P1	54019	bcgsc.ca	37	21	20617291	20617291	+	IGR	SNP	G	G	T	rs9980261	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:20617291G>T								AP000431.2 (110550 upstream) : AP000855.4 (56638 downstream)																							CTGGGCTACAGACTACCTGTT	0.587													T|||	1895	0.378395	0.5825	0.3343	5008	,	,		18917	0.4107		0.2654	False		,,,				2504	0.2168				.													.	.			0			.																																									SO:0001628	intergenic_variant	54019	.			GCTACAGACTACC																													21.37:g.20617291G>T			48	0	0		46	0.17	8	.	0		0		RNA	SNP		37																																																																																					0	0.587										
THUMPD1P1	391276	bcgsc.ca	37	21	30274198	30274198	+	IGR	SNP	G	G	A	rs2248250	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:30274198G>A								N6AMT1 (16505 upstream) : LTN1 (26267 downstream)																							CGGATTAGACGTTCTTTTCCG	0.438													G|||	401	0.0800719	0.1778	0.0504	5008	,	,		17273	0.003		0.0974	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	391276	.			TTAGACGTTCTTT																													21.37:g.30274198G>A			36	0	0		32	0.16	5	.	0		0		RNA	SNP		37																																																																																					0	0.438										
THUMPD1P1	391276	bcgsc.ca	37	21	30274205	30274205	+	IGR	SNP	T	T	C	rs2738935	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:30274205T>C								N6AMT1 (16512 upstream) : LTN1 (26260 downstream)																							GACGTTCTTTTCCGCCCTAGC	0.443													T|||	401	0.0800719	0.1778	0.0504	5008	,	,		17573	0.003		0.0974	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	391276	.			TTCTTTTCCGCCC																													21.37:g.30274205T>C			33	0	0		28	0.14	4	.	0		0		RNA	SNP		37																																																																																					0	0.443										
THUMPD1P1	391276	bcgsc.ca	37	21	30275638	30275638	+	IGR	SNP	C	C	T	rs2248470	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:30275638C>T								N6AMT1 (17945 upstream) : LTN1 (24827 downstream)																							CTGATGAAGGCGACGTTATTT	0.438													C|||	401	0.0800719	0.177	0.0504	5008	,	,		20912	0.004		0.0974	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	391276	.			TGAAGGCGACGTT																													21.37:g.30275638C>T			65	0	0		77	0.06	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.438										
THUMPD1P1	391276	bcgsc.ca	37	21	30275705	30275705	+	IGR	SNP	G	G	A	rs2705643	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:30275705G>A								N6AMT1 (18012 upstream) : LTN1 (24760 downstream)																							ATGCCTCAATGTCACCAACTT	0.473													G|||	233	0.0465256	0.053	0.0461	5008	,	,		21039	0.003		0.0974	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	391276	.			CTCAATGTCACCA																													21.37:g.30275705G>A			56	0.0178571429	1		77	0.12	9	.	0		0		RNA	SNP		37																																																																																					0	0.473										
TIAM1	7074	bcgsc.ca	37	21	32638549	32638550	+	Missense_Mutation	DNP	CC	CC	AT	rs2070418|rs386817934|rs2070417	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:32638549_32638550CC>AT	ENST00000286827.3	-	5	1210_1211	c.739_740GG>AT	c.(739-741)GGg>ATg	p.G247M	TIAM1_ENST00000541036.1_Missense_Mutation_p.G247M|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	247			G -> R (in dbSNP:rs2070418).|G -> V (in dbSNP:rs2070417).	G -> M (in Ref. 1; AAA98443). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CCCCGGCCCCCCGTTTGCTGTC	0.535																																					p.G247M													.	TIAM1	522		0			c.G739A																																									SO:0001583	missense	7074	exon5			GGCCCCCCGTTTG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.739_740delinsAT	21.37:g.32638549_32638550delinsAT	ENSP00000286827:p.Gly247Met		202	0	0		234	0.06	13	NM_003253	19	0.00	0	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	DNP	ENST00000286827.3	37	CCDS13609.1																																																																																					0.535	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000192552.1		NM_003253	
PAXBP1	94104	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	34123334	34123336	+	In_Frame_Del	DEL	ACG	ACG	-			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	ACG	ACG					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:34123334_34123336delACG	ENST00000331923.4	-	10	1804_1806	c.1615_1617delCGT	c.(1615-1617)cgtdel	p.R540del	PAXBP1_ENST00000290178.4_In_Frame_Del_p.R540del	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	540	Necessary and sufficient for interaction with PAX7. {ECO:0000250}.				muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGCTTGTCTACGACGAGTCCTA	0.424																																					p.539_540del													.	.			0			c.1616_1618del																																									SO:0001651	inframe_deletion	94104	exon10			TTGTCTACGACGA	AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1615_1617delCGT	21.37:g.34123337_34123339delACG	ENSP00000328992:p.Arg540del		158	0	0		172	0.15	26	NM_013329	87	0.00	0	D3DSE7|Q96DU8|Q9NYQ0	In_Frame_Del	DEL	ENST00000331923.4	37	CCDS13619.1																																																																																					0.424	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000139563.1		NM_013329	
KRTAP12-2	353323	bcgsc.ca	37	21	46086718	46086719	+	Missense_Mutation	DNP	GA	GA	CG	rs7275281|rs368303093|rs7276859	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	GA	GA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr21:46086718_46086719GA>CG	ENST00000360770.3	-	1	125_126	c.85_86TC>CG	c.(85-87)TCc>CGc	p.S29R	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						TGCCTGGCAGGAGCTGGGCACA	0.678																																					p.S29R													.	KRTAP12-2	10		0			c.T85C																																									SO:0001583	missense	353323	exon1			TGGCAGGAGCTGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.85_86delinsCG	21.37:g.46086718_46086719delinsCG	ENSP00000354001:p.Ser29Arg		77	0.012987013	1		94	0.11	10	NM_181684	0		0	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	DNP	ENST00000360770.3	37	CCDS42965.1																																																																																					0.678	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000128039.1		NM_181684	
SLC9B1P4	644768	bcgsc.ca	37	22	16940793	16940793	+	IGR	SNP	C	C	T	rs150627359	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:16940793C>T								AP000539.2 (364602 upstream) : KB-67B5.17 (61155 downstream)																							CATTTTCTTGCGACACCATTG	0.373													C|||	68	0.0135783	0.0106	0.0259	5008	,	,		19886	0.0		0.0328	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001628	intergenic_variant	644768	.			TTCTTGCGACACC																													22.37:g.16940793C>T			144	0	0		153	0.08	12	.	0		0		RNA	SNP		37																																																																																					0	0.373										
RIMBP3	85376	bcgsc.ca;mdanderson.org	37	22	20457841	20457841	+	Missense_Mutation	SNP	T	T	C	rs202034782	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:20457841T>C	ENST00000426804.1	-	1	3945	c.3461A>G	c.(3460-3462)cAg>cGg	p.Q1154R	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1154	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GAGGGGCACCTGTAGCTGGGA	0.557																																					p.Q1154R													.	RIMBP3	42		0			c.A3461G							T	ARG/GLN	4,4134		0,4,2065	81.0	84.0	83.0		3461	1.0	0.0	22		83	69,8347		0,69,4139	no	missense	RIMBP3	NM_015672.1	43	0,73,6204	CC,CT,TT		0.8199,0.0967,0.5815	benign	1154/1640	20457841	73,12481	2069	4208	6277	SO:0001583	missense	85376	exon1			GGCACCTGTAGCT	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3461A>G	22.37:g.20457841T>C	ENSP00000391564:p.Gln1154Arg		1100	0	0		972	0.03	31	NM_015672	3	0.00	0	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	T	5.252	0.231948	0.09969	9.67E-4	0.008199	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.33438	1.41	3.42	1.03	0.20045	Fibronectin, type III (2);	0.154983	0.44285	D	0.000478	T	0.14356	0.0347	L	0.33189	0.99	0.28898	N	0.893448	B	0.30686	0.29	B	0.28638	0.092	T	0.08932	-1.0698	10	0.52906	T	0.07	-13.6718	8.407	0.32621	0.0:0.0:0.3851:0.6149	.	1060	Q9UFD9	RIM3A_HUMAN	R	1060;1154	ENSP00000391564:Q1154R	ENSP00000347318:Q1060R	Q	-	2	0	RIMBP3	18837841	0.943000	0.32029	0.030000	0.17652	0.368000	0.29767	1.508000	0.35769	0.040000	0.15660	0.155000	0.16302	CAG			0.557	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318945.2		NM_015672	
LRRC74B	400891	ucsc.edu;bcgsc.ca;mdanderson.org	37	22	21407656	21407656	+	Missense_Mutation	SNP	T	T	C	rs59837066	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:21407656T>C	ENST00000342608.4	+	6	767	c.740T>C	c.(739-741)aTc>aCc	p.I247T	AC002472.13_ENST00000543388.1_3'UTR|AC002472.13_ENST00000497328.1_3'UTR																lung(2)	2						TAGGCAAACATCTTCCTTAAA	0.537													t|||	42	0.00838658	0.0136	0.0115	5008	,	,		19048	0.0		0.007	False		,,,				2504	0.0092				.													.	.			0			.																																									SO:0001583	missense	0	.			CAAACATCTTCCT																												ENST00000342608.4:c.740T>C	22.37:g.21407656T>C	ENSP00000341179:p.Ile247Thr		137	0	0		138	0.11	15	.	0		0		Missense_Mutation	SNP	ENST00000342608.4	37		21	0.009615384615384616	9	0.018292682926829267	6	0.016574585635359115	0	0.0	6	0.0079155672823219	T	11.41	1.631298	0.28978	.	.	ENSG00000187905	ENST00000342608;ENST00000442047	T;T	0.50277	0.75;0.75	4.88	4.88	0.63580	.	.	.	.	.	T	0.24812	0.0602	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06935	-1.0799	6	0.13108	T	0.6	-6.4358	11.0751	0.48027	0.0:0.0:0.0:1.0	rs59837066	.	.	.	T	247	ENSP00000341179:I247T;ENSP00000394078:I247T	ENSP00000341179:I247T	I	+	2	0	AC002472.13	19737656	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	2.149000	0.42244	2.193000	0.70182	0.459000	0.35465	ATC			0.537	AC002472.13-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
IGLV4-60	28785	broad.mit.edu	37	22	22516884	22516884	+	RNA	DEL	C	C	-	rs34221567	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:22516884delC	ENST00000390284.2	+	0	172									immunoglobulin lambda variable 4-60																		CGCATGGCATCAGCAGCAGCC	0.567													C|C|-|deletion	905	0.180711	0.1074	0.2406	5008	,	,		20423	0.0575		0.4195	False		,,,				2504	0.1186				.													.	.			0			.									613,3457		73,467,1495	70.0	58.0	62.0			-5.7	0.0	22	dbSNP_126	82	3051,5071		628,1795,1638	no	intergenic				701,2262,3133	A1A1,A1R,RR		37.5646,15.0614,30.0525			22516884	3664,8528	2043	3697	5740			0	.			TGGCATCAGCAGC	Z73667		22q11.2	2012-02-08			ENSG00000211639	ENSG00000211639		"""Immunoglobulins / IGL locus"""	5920	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000150851		22.37:g.22516884delC			263	0	0		196	0.07	14	.	56	0.00	0		RNA	DEL	ENST00000390284.2	37																																																																																						0.567	IGLV4-60-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000320328.1		NG_000002	
IGLV4-60	28785	bcgsc.ca	37	22	22516998	22516998	+	RNA	SNP	C	C	T	rs2073453	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:22516998C>T	ENST00000390284.2	+	0	286									immunoglobulin lambda variable 4-60																		TGGGGCTGACCGCTACCTCAC	0.532													C|||	1665	0.332468	0.1747	0.3127	5008	,	,		18142	0.4454		0.4513	False		,,,				2504	0.3211				.													.	.			0			.							C		794,3238		82,630,1304	56.0	57.0	57.0			-1.0	0.0	22	dbSNP_96	57	3400,4956		730,1940,1508	no	intergenic				812,2570,2812	TT,TC,CC		40.6893,19.6925,33.8553			22516998	4194,8194	2016	4178	6194			28785	.			GCTGACCGCTACC	Z73667		22q11.2	2012-02-08			ENSG00000211639	ENSG00000211639		"""Immunoglobulins / IGL locus"""	5920	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000150851		22.37:g.22516998C>T			140	0	0		121	0.07	8	.	62	0.00	0		RNA	SNP	ENST00000390284.2	37																																																																																						0.532	IGLV4-60-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000320328.1		NG_000002	
IGLV11-55	28770	bcgsc.ca	37	22	22556368	22556368	+	RNA	SNP	C	C	T	rs9306341	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:22556368C>T	ENST00000390286.2	+	0	194									immunoglobulin lambda variable 11-55 (non-functional)																		CAGCAGAAGCCAGGGAGCTCT	0.567											OREG0026354	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2784	0.555911	0.7292	0.4539	5008	,	,		18569	0.3641		0.493	False		,,,				2504	0.6564				.													.	.			0			.							C		2651,1237		913,825,206	67.0	73.0	71.0			2.0	0.7	22	dbSNP_119	71	4058,4238		981,2096,1071	no	intergenic				1894,2921,1277	TT,TC,CC		48.9151,31.8158,44.936			22556368	6709,5475	1944	4148	6092			28770	.			AGAAGCCAGGGAG	D86996		22q11.2	2012-02-08	2008-09-15		ENSG00000211641	ENSG00000211641		"""Immunoglobulins / IGL locus"""	5886	other	immunoglobulin gene			"""immunoglobulin lambda variable 11-55"""				Standard	NG_000002		Approved				OTTHUMG00000150995		22.37:g.22556368C>T			76	0	0	757	98	0.07	7	.	0		0		RNA	SNP	ENST00000390286.2	37																																																																																						0.567	IGLV11-55-001	KNOWN	basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000320860.3		NG_000002	
TOP3BP1	23751	bcgsc.ca	37	22	22577869	22577869	+	IGR	SNP	A	A	G	rs201277699	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:22577869A>G								IGLV10-54 (8209 upstream) : VPREB1 (21217 downstream)																							GTGTCGGCGGACACCCGCACG	0.652													N|||	1970	0.393371	0.348	0.3775	5008	,	,		16414	0.4683		0.4215	False		,,,				2504	0.3599				.													.	.			0			.																																									SO:0001628	intergenic_variant	23751	.			CGGCGGACACCCG																													22.37:g.22577869A>G			341	0	0		289	0.07	21	.	0		0		RNA	SNP		37																																																																																					0	0.652										
IGLV3-12	28802	bcgsc.ca;mdanderson.org	37	22	23114327	23114327	+	RNA	SNP	T	T	C	rs6003299	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:23114327T>C	ENST00000390313.2	+	0	11									immunoglobulin lambda variable 3-12																		GCCTCAGCCATGGCCTGGACC	0.622													.|||	3048	0.608626	0.5356	0.5461	5008	,	,		15273	0.9444		0.4205	False		,,,				2504	0.5992				.													.	.			0			.																																											28802	.			CAGCCATGGCCTG	Z73658		22q11.2	2012-02-08			ENSG00000211667	ENSG00000211667		"""Immunoglobulins / IGL locus"""	5898	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000151233		22.37:g.23114327T>C			133	0	0		102	0.17	17	.	2	0.00	0		RNA	SNP	ENST00000390313.2	37																																																																																						0.622	IGLV3-12-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000321838.1		NG_000002	
IGLV3-12	28802	bcgsc.ca;mdanderson.org	37	22	23114350	23114350	+	RNA	SNP	A	A	G	rs5996382	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:23114350A>G	ENST00000390313.2	+	0	34									immunoglobulin lambda variable 3-12																		TCTCCTCCTCAGCCTCCTCGC	0.627													.|||	3048	0.608626	0.5356	0.5461	5008	,	,		14883	0.9444		0.4205	False		,,,				2504	0.5992				.													.	.			0			.																																											28802	.			CTCCTCAGCCTCC	Z73658		22q11.2	2012-02-08			ENSG00000211667	ENSG00000211667		"""Immunoglobulins / IGL locus"""	5898	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000151233		22.37:g.23114350A>G			150	0.0066666667	1		110	0.21	23	.	1	0.00	0		RNA	SNP	ENST00000390313.2	37																																																																																						0.627	IGLV3-12-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000321838.1		NG_000002	
IGLV3-12	28802	bcgsc.ca;mdanderson.org	37	22	23114993	23114993	+	RNA	SNP	G	G	A	rs2073451	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:23114993G>A	ENST00000390313.2	+	0	274									immunoglobulin lambda variable 3-12																		AGGGAACACCGCCACCCTAAC	0.577													g|||	1957	0.390775	0.3533	0.4438	5008	,	,		14028	0.5694		0.3111	False		,,,				2504	0.3016				.													.	.			0			.							G		1173,2877		163,847,1015	59.0	59.0	59.0			2.7	0.7	22	dbSNP_96	59	2397,5937		350,1697,2120	no	intergenic				513,2544,3135	AA,AG,GG		28.7617,28.963,28.8275			23114993	3570,8814	2025	4167	6192			28802	.			AACACCGCCACCC	Z73658		22q11.2	2012-02-08			ENSG00000211667	ENSG00000211667		"""Immunoglobulins / IGL locus"""	5898	other	immunoglobulin gene							Standard	NG_000002		Approved				OTTHUMG00000151233		22.37:g.23114993G>A			98	0	0		93	0.15	14	.	4	0.00	0		RNA	SNP	ENST00000390313.2	37																																																																																						0.577	IGLV3-12-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000321838.1		NG_000002	
RASL10A	10633	bcgsc.ca;mdanderson.org	37	22	29707888	29707888	+	IGR	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:29707888C>T	ENST00000216101.6	-	0	1490				RASL10A_ENST00000608559.1_5'Flank|GAS2L1_ENST00000407647.2_Missense_Mutation_p.P483S|GAS2L1_ENST00000406549.3_Intron|GAS2L1_ENST00000407854.1_Missense_Mutation_p.P483S|GAS2L1_ENST00000360113.2_3'UTR|GAS2L1_ENST00000341313.6_3'UTR|GAS2L1_ENST00000403764.1_Missense_Mutation_p.P483S|GAS2L1_ENST00000471961.1_Missense_Mutation_p.P483S	NM_006477.4	NP_006468.1	Q92737	RSLAA_HUMAN	RAS-like, family 10, member A						small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)	1						CCTGCAGCACCCCGGCTTTCC	0.711																																					.													.	GAS2L1	54		0			.												9.0	13.0	11.0					22																	29707888		1986	4055	6041	SO:0001628	intergenic_variant	10634	.			CAGCACCCCGGCT	Y07847	CCDS13854.1	22q12.2	2014-05-09			ENSG00000100276	ENSG00000100276			16954	protein-coding gene	gene with protein product		602220				8975699, 15731001	Standard	NM_006477		Approved	RRP22	uc031rxl.1	Q92737	OTTHUMG00000151106		22.37:g.29707888C>T			18	0	0		17	0.29	5	.	65	0.09	6	Q49AU5|Q6PI03	Missense_Mutation	SNP	ENST00000216101.6	37	CCDS13854.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.647|0.647	-0.810903|-0.810903	0.02798|0.02798	.|.	.|.	ENSG00000185340|ENSG00000185340	ENST00000333679|ENST00000407647;ENST00000403764;ENST00000471961;ENST00000407854	.|T;T;T;T	.|0.55588	.|0.51;0.51;0.51;0.51	3.47|3.47	-0.141|-0.141	0.13452|0.13452	.|.	0.885835|0.885835	0.09227|0.09227	N|U	0.831098|0.831098	T|T	0.26702|0.26702	0.0653|0.0653	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B|B	0.02656|0.02656	0.0;0.0|0.0	B;B|B	0.01281|0.01281	0.0;0.0|0.0	T|T	0.16335|0.16335	-1.0406|-1.0406	9|10	0.41790|0.27785	T|T	0.15|0.31	-0.5555|-0.5555	3.8535|3.8535	0.08965|0.08965	0.0:0.3121:0.3736:0.3143|0.0:0.3121:0.3736:0.3143	.|.	483;483|483	A0A5E8;Q99501|E7EQM6	.;GA2L1_HUMAN|.	L|S	482|483	.|ENSP00000385554:P483S;ENSP00000385358:P483S;ENSP00000450152:P483S;ENSP00000385023:P483S	ENSP00000332834:P482L|ENSP00000385358:P483S	P|P	+|+	2|1	0|0	GAS2L1|GAS2L1	28037888|28037888	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.033000|0.033000	0.12548|0.12548	-0.232000|-0.232000	0.09055|0.09055	-0.134000|-0.134000	0.11516|0.11516	0.491000|0.491000	0.48974|0.48974	CCC|CCC			0.711	RASL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000321342.1			
LIMK2	3985	ucsc.edu	37	22	31655980	31655980	+	Silent	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:31655980G>A	ENST00000331728.4	+	5	582	c.468G>A	c.(466-468)ccG>ccA	p.P156P	LIMK2_ENST00000333611.4_Silent_p.P135P|LIMK2_ENST00000406516.1_Silent_p.P78P|LIMK2_ENST00000444929.2_Intron|LIMK2_ENST00000340552.4_Silent_p.P135P	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	156	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.P156P(1)		endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						TCTCCATGCCGGCCACCACTG	0.562																																					p.P156P													LIMK2,colon,carcinoma,0,1	LIMK2	101	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A												67.0	59.0	62.0					22																	31655980		2203	4300	6503	SO:0001819	synonymous_variant	3985	exon5			CATGCCGGCCACC	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.468G>A	22.37:g.31655980G>A			52	0.0192307692	1		43	0.09	4	NM_005569	53	0.00	0	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Silent	SNP	ENST00000331728.4	37	CCDS13891.1																																																																																					0.562	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000321911.1		NM_016733	
RP1-32I10.10	0	bcgsc.ca	37	22	44761797	44761797	+	Missense_Mutation	SNP	T	T	A	rs5765809	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:44761797T>A	ENST00000406912.1	+	2	239	c.175T>A	c.(175-177)Tta>Ata	p.L59I																	breast(1)	1						agctatgtgcttagacactcc	0.498													T|||	1857	0.370807	0.7148	0.2277	5008	,	,		17528	0.1558		0.3539	False		,,,				2504	0.2464				.													.	.			0			.																																									SO:0001583	missense	0	.			ATGTGCTTAGACA																												ENST00000406912.1:c.175T>A	22.37:g.44761797T>A	ENSP00000384566:p.Leu59Ile		138	0	0		141	0.06	8	.	0		0		Missense_Mutation	SNP	ENST00000406912.1	37		795	0.364010989010989	361	0.733739837398374	78	0.2154696132596685	89	0.1555944055944056	267	0.35224274406332456	T	7.194	0.592155	0.13812	.	.	ENSG00000220702	ENST00000406912	.	.	.	0.158	0.158	0.14942	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.36625	-0.9740	3	0.87932	D	0	.	.	.	.	rs5765809;rs60112594;rs5765809	.	.	.	I	59	.	ENSP00000384566:L59I	L	+	1	2	RP1-32I10.10	43140461	0.161000	0.22892	0.089000	0.20774	0.090000	0.18270	0.215000	0.17562	0.175000	0.19841	0.172000	0.16884	TTA			0.498	RP1-32I10.10-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000318221.1			
Unknown	0	bcgsc.ca	37	22	51193572	51193572	+	IGR	SNP	A	A	G	rs138661035	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:51193572A>G								ACR (9810 upstream) : RABL2B (12356 downstream)																							CGAGCCTATTATTGGTGAGAA	0.438													A|||	199	0.0397364	0.0083	0.0389	5008	,	,		19388	0.0308		0.0785	False		,,,				2504	0.0521				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTATTATTGGTG																													22.37:g.51193572A>G			143	0	0		137	0.12	16	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.438										
Unknown	0	bcgsc.ca	37	22	51193629	51193629	+	IGR	SNP	A	A	G	rs142680588	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr22:51193629A>G								ACR (9867 upstream) : RABL2B (12299 downstream)																							CCTCACCTATACGGCATATTC	0.443													A|||	251	0.0501198	0.0454	0.0432	5008	,	,		19267	0.0308		0.0785	False		,,,				2504	0.0521				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACCTATACGGCAT																													22.37:g.51193629A>G			253	0	0		232	0.10	24	.	9	0.00	0		RNA	SNP		37																																																																																					0	0.443										
FANCD2P2	101929530	bcgsc.ca	37	3	11915154	11915154	+	IGR	SNP	A	A	G	rs3732701	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:11915154A>G								TAMM41 (26761 upstream) : RN7SL147P (79109 downstream)																							TCCCCTCAGCAAATACGAAAA	0.393													A|||	740	0.147764	0.0802	0.1427	5008	,	,		17354	0.3363		0.1074	False		,,,				2504	0.09				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCAGCAAATACG																													3.37:g.11915154A>G			83	0	0		69	0.14	10	.	0		0		RNA	SNP		37																																																																																					0	0.393										
NEK10	152110	bcgsc.ca;mdanderson.org	37	3	27204052	27204052	+	Silent	SNP	G	G	A	rs17854381	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:27204052G>A	ENST00000429845.2	-	32	3272	c.2910C>T	c.(2908-2910)caC>caT	p.H970H	NEK10_ENST00000498182.1_Intron|NEK10_ENST00000357467.2_Silent_p.H367H|NEK10_ENST00000295720.6_Silent_p.H282H|NEK10_ENST00000383770.3_Intron|NEK10_ENST00000383771.4_Silent_p.H282H			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	970					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CCCTGAGCATGTGGGGTGGCA	0.433													G|||	1005	0.200679	0.1006	0.3156	5008	,	,		19478	0.0853		0.2783	False		,,,				2504	0.2935				.													NEK10_ENST00000429845,NS,carcinoma,0,1	.		1	0			.							G		628,3778	271.9+/-270.5	56,516,1631	85.0	83.0	84.0			4.6	1.0	3	dbSNP_123	84	2392,6208	398.2+/-346.0	352,1688,2260	no	intergenic				408,2204,3891	AA,AG,GG		27.814,14.2533,23.2201			27204052	3020,9986	2203	4300	6503	SO:0001819	synonymous_variant	152110	.			GAGCATGTGGGGT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2910C>T	3.37:g.27204052G>A			145	0.0068965517	1		127	0.08	10	.	0		0	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37																																																																																						0.433	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000438156.1		NM_152534	
NEK10	152110	bcgsc.ca	37	3	27216197	27216197	+	Missense_Mutation	SNP	C	C	T	rs55780680	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:27216197C>T	ENST00000429845.2	-	28	2995	c.2633G>A	c.(2632-2634)aGg>aAg	p.R878K	NEK10_ENST00000498182.1_5'UTR|NEK10_ENST00000357467.2_Missense_Mutation_p.R275K|NEK10_ENST00000295720.6_Missense_Mutation_p.R190K|NEK10_ENST00000383770.3_Missense_Mutation_p.R190K|NEK10_ENST00000383771.4_Missense_Mutation_p.R190K			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	878					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R878K(1)|p.R878M(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GTCACAGGCCCTGTCTTCGTC	0.517													C|||	478	0.0954473	0.3495	0.0202	5008	,	,		17847	0.0		0.002	False		,,,				2504	0.0				.													NEK10,NS,carcinoma,0,2	.		2	2	Substitution - Missense(2)	lung(1)|stomach(1)	.							C		1245,3161	429.1+/-342.1	173,899,1131	140.0	133.0	135.0			5.9	1.0	3	dbSNP_129	135	13,8587	9.1+/-34.3	0,13,4287	no	intergenic				173,912,5418	TT,TC,CC		0.1512,28.2569,9.6725			27216197	1258,11748	2203	4300	6503	SO:0001583	missense	152110	.			CAGGCCCTGTCTT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2633G>A	3.37:g.27216197C>T	ENSP00000395849:p.Arg878Lys		268	0	0		235	0.03	8	.	0		0	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		183	0.08379120879120878	176	0.35772357723577236	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	11.95	1.792486	0.31685	0.282569	0.001512	ENSG00000163491	ENST00000295720;ENST00000383771;ENST00000383770;ENST00000357467	T;T;T;T	0.72615	2.83;2.89;3.12;-0.67	5.91	5.91	0.95273	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46131	P	0.0011179999999999524	B;B;B	0.17038	0.02;0.008;0.01	B;B;B	0.14578	0.011;0.011;0.005	T	0.07693	-1.0759	7	0.38643	T	0.18	.	11.2483	0.49010	0.0:0.8758:0.0:0.1242	rs55780680	190;190;275	Q6ZWH5-5;Q6ZWH5-7;Q8N774	.;.;.	K	190;190;190;275	ENSP00000295720:R190K;ENSP00000373281:R190K;ENSP00000373280:R190K;ENSP00000350059:R275K	ENSP00000295720:R190K	R	-	2	0	NEK10	27191201	0.999000	0.42202	1.000000	0.80357	0.848000	0.48234	1.083000	0.30815	2.807000	0.96579	0.557000	0.71058	AGG			0.517	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000438156.1		NM_152534	
NEK10	152110	bcgsc.ca	37	3	27243045	27243045	+	Silent	SNP	G	G	C	rs17680166	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:27243045G>C	ENST00000429845.2	-	26	2609	c.2247C>G	c.(2245-2247)gtC>gtG	p.V749V	NEK10_ENST00000357467.2_Silent_p.V146V|NEK10_ENST00000295720.6_Silent_p.V61V|NEK10_ENST00000383770.3_Silent_p.V61V|NEK10_ENST00000383771.4_Silent_p.V61V			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	749					positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TACCTTCTGGGACTGGTTCAT	0.418													C|||	1027	0.205072	0.1059	0.3098	5008	,	,		17149	0.0863		0.2833	False		,,,				2504	0.3067				.													.	.			0			.							C		652,3754	765.3+/-413.3	55,542,1606	136.0	126.0	130.0			1.9	1.0	3	dbSNP_123	130	2367,6233	702.2+/-405.3	358,1651,2291	no	intergenic				413,2193,3897	CC,CG,GG		27.5233,14.798,23.2124			27243045	3019,9987	2203	4300	6503	SO:0001819	synonymous_variant	152110	.			TTCTGGGACTGGT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2247C>G	3.37:g.27243045G>C			184	0	0		169	0.04	6	.	0		0	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37																																																																																						0.418	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000438156.1		NM_152534	
THRAP3P1	391524	bcgsc.ca	37	3	31494587	31494587	+	IGR	SNP	G	G	A	rs17027714	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:31494587G>A								AC099540.1 (57064 upstream) : STT3B (79542 downstream)																							TTCCGTGGGCGCAACAGAGGC	0.493													G|||	1633	0.326078	0.1884	0.3357	5008	,	,		17732	0.623		0.2813	False		,,,				2504	0.2454				.													.	.			0			.																																									SO:0001628	intergenic_variant	391524	.			GTGGGCGCAACAG																													3.37:g.31494587G>A			57	0	0		57	0.12	7	.	0		0		RNA	SNP		37																																																																																					0	0.493										
THRAP3P1	391524	bcgsc.ca	37	3	31494993	31494993	+	IGR	SNP	C	C	T	rs9824199	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:31494993C>T								AC099540.1 (57470 upstream) : STT3B (79136 downstream)																							ATGCCACCTACGGCACTGGTT	0.572													C|||	2304	0.460064	0.5545	0.3602	5008	,	,		18579	0.6677		0.2853	False		,,,				2504	0.3691				.													.	.			0			.																																									SO:0001628	intergenic_variant	391524	.			CACCTACGGCACT																													3.37:g.31494993C>T			68	0	0		51	0.12	6	.	0		0		RNA	SNP		37																																																																																					0	0.572										
THRAP3P1	391524	bcgsc.ca	37	3	31496145	31496145	+	IGR	SNP	T	T	C	rs9849739	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:31496145T>C								AC099540.1 (58622 upstream) : STT3B (77984 downstream)																							TGTTCCATTTTCCAGCACATA	0.463													T|||	850	0.169728	0.3162	0.1542	5008	,	,		19716	0.0565		0.162	False		,,,				2504	0.1074				.													.	.			0			.																																									SO:0001628	intergenic_variant	391524	.			CCATTTTCCAGCA																													3.37:g.31496145T>C			185	0	0		138	0.04	6	.	0		0		RNA	SNP		37																																																																																					0	0.463										
IGBP1P3	391526	bcgsc.ca	37	3	32662531	32662531	+	IGR	SNP	T	T	C	rs6550143	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662531T>C								DYNC1LI1 (50165 upstream) : CNOT10 (64105 downstream)																							TTTCTGAATTTCTCTGGTGTT	0.458													C|||	2161	0.43151	0.8767	0.2219	5008	,	,		21630	0.3095		0.2525	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			TGAATTTCTCTGG																													3.37:g.32662531T>C			108	0	0		60	0.12	7	.	0		0		RNA	SNP		37																																																																																					0	0.458										
IGBP1P3	391526	bcgsc.ca	37	3	32662803	32662803	+	IGR	SNP	C	C	A	rs59067676	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662803C>A								DYNC1LI1 (50437 upstream) : CNOT10 (63833 downstream)																							GTATCAATCCCCCTTTGAAGG	0.423													A|||	2087	0.416733	0.826	0.2118	5008	,	,		20294	0.3095		0.2525	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			CAATCCCCCTTTG																													3.37:g.32662803C>A			176	0.0056818182	1		132	0.11	15	.	0		0		RNA	SNP		37																																																																																					0	0.423										
IGBP1P3	391526	bcgsc.ca	37	3	32662807	32662807	+	IGR	SNP	T	T	C	rs58963522	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662807T>C								DYNC1LI1 (50441 upstream) : CNOT10 (63829 downstream)																							CAATCCCCCTTTGAAGGTGAA	0.418													C|||	2087	0.416733	0.826	0.2118	5008	,	,		20494	0.3095		0.2525	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			CCCCCTTTGAAGG																													3.37:g.32662807T>C			186	0.0053763441	1		139	0.11	15	.	0		0		RNA	SNP		37																																																																																					0	0.418										
IGBP1P3	391526	bcgsc.ca	37	3	32662919	32662919	+	IGR	SNP	C	C	T	rs34045705	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662919C>T								DYNC1LI1 (50553 upstream) : CNOT10 (63717 downstream)																							CTGCTTGTATCTCTCTATTTT	0.418													C|||	2087	0.416733	0.826	0.2118	5008	,	,		20357	0.3095		0.2525	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			TTGTATCTCTCTA																													3.37:g.32662919C>T			182	0.0054945055	1		169	0.12	20	.	0		0		RNA	SNP		37																																																																																					0	0.418										
IGBP1P3	391526	bcgsc.ca	37	3	32662938	32662938	+	IGR	SNP	T	T	C	rs35370637	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662938T>C								DYNC1LI1 (50572 upstream) : CNOT10 (63698 downstream)																							TTAGCCTGCCTTTGAGATGCC	0.438													T|||	1334	0.266374	0.4024	0.1527	5008	,	,		20133	0.251		0.2137	False		,,,				2504	0.2331				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			CCTGCCTTTGAGA																													3.37:g.32662938T>C			164	0	0		168	0.07	12	.	0		0		RNA	SNP		37																																																																																					0	0.438										
IGBP1P3	391526	bcgsc.ca	37	3	32662960	32662960	+	IGR	SNP	A	A	G	rs35066348|rs386659960	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:32662960A>G								DYNC1LI1 (50594 upstream) : CNOT10 (63676 downstream)																							TAGCAACGAGACTAGGATAAG	0.428													G|||	2089	0.417133	0.8275	0.2118	5008	,	,		20215	0.3095		0.2525	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	391526	.			AACGAGACTAGGA																													3.37:g.32662960A>G			162	0	0		161	0.14	23	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.428										
DSTNP4	729454	bcgsc.ca	37	3	39255730	39255730	+	IGR	SNP	G	G	A	rs7643880	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:39255730G>A								XIRP1 (21643 upstream) : CX3CR1 (49254 downstream)																							CACATTTTTTGTGACATAAAA	0.453													A|||	2634	0.525958	0.7534	0.3934	5008	,	,		18005	0.4067		0.5398	False		,,,				2504	0.4213				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTTTGTGACAT																													3.37:g.39255730G>A			29	0	0		28	0.18	5	.	0		0		RNA	SNP		37																																																																																					0	0.453										
NFU1P1	100132681	bcgsc.ca	37	3	39686013	39686013	+	IGR	SNP	A	A	T	rs78908069	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:39686013A>T								MOBP (118912 upstream) : MYRIP (164391 downstream)																							GACGTAATCTACAAAGGTTTT	0.408													A|||	100	0.0199681	0.0023	0.0375	5008	,	,		20288	0.0		0.0547	False		,,,				2504	0.0164				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAATCTACAAAGG																													3.37:g.39686013A>T			90	0	0		117	0.08	9	.	0		0		RNA	SNP		37																																																																																					0	0.408										
SALL4P6	391530	bcgsc.ca	37	3	42363697	42363697	+	IGR	SNP	C	C	T	rs139639533	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:42363697C>T								CCK (55998 upstream) : LYZL4 (74872 downstream)																							TGGTGCTCTTCGCATTCACGG	0.527													C|||	54	0.0107827	0.0023	0.0173	5008	,	,		19867	0.0179		0.0199	False		,,,				2504	0.001				.													.	.			0			.																																									SO:0001628	intergenic_variant	391530	.			GCTCTTCGCATTC																													3.37:g.42363697C>T			28	0	0		28	0.18	5	.	0		0		RNA	SNP		37																																																																																					0	0.527										
MYLKP1	9430	bcgsc.ca	37	3	75377715	75377715	+	IGR	SNP	C	C	T	rs4677496	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:75377715C>T								MIR4444-1 (114015 upstream) : AC117481.1 (17574 downstream)																							TGGGAGAGGACGATGAACTTG	0.582													T|||	1911	0.381589	0.5938	0.3314	5008	,	,		18563	0.5308		0.0815	False		,,,				2504	0.2853				.													.	.			0			.																																									SO:0001628	intergenic_variant	9430	.			AGAGGACGATGAA																													3.37:g.75377715C>T			56	0	0		60	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.582										
RAP1BP2	100128179	bcgsc.ca	37	3	103782249	103782249	+	IGR	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:103782249G>T								AC016970.1 (8609 upstream) : None (None downstream)																							AGATGAAAGAGTTGTAGAAAA	0.313																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAAAGAGTTGTAG																													3.37:g.103782249G>T			38	0	0		31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.313										
EIF4BP8	339881	bcgsc.ca	37	3	122380888	122380888	+	IGR	SNP	C	C	T	rs790117	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:122380888C>T								PARP15 (22994 upstream) : PARP14 (18576 downstream)																							GCCCCTCCACCAAAGGAGAAT	0.478													C|||	2318	0.462859	0.5053	0.4726	5008	,	,		20993	0.5109		0.4056	False		,,,				2504	0.408				.													.	.			0			.																																									SO:0001628	intergenic_variant	339881	.			CTCCACCAAAGGA																													3.37:g.122380888C>T			77	0	0		89	0.09	8	.	0		0		RNA	SNP		37																																																																																					0	0.478										
EIF4BP8	339881	bcgsc.ca	37	3	122380923	122380923	+	IGR	SNP	G	G	C	rs790116	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:122380923G>C								PARP15 (23029 upstream) : PARP14 (18541 downstream)																							AAGTTCTAACGCTCCTGCTCC	0.512													C|||	2318	0.462859	0.5053	0.4726	5008	,	,		20699	0.5109		0.4056	False		,,,				2504	0.408				.													.	.			0			.																																									SO:0001628	intergenic_variant	339881	.			TCTAACGCTCCTG																													3.37:g.122380923G>C			80	0	0		89	0.11	10	.	0		0		RNA	SNP		37																																																																																					0	0.512										
LOC653712	653712	bcgsc.ca	37	3	128580585	128580585	+	RNA	SNP	C	C	A	rs789247	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:128580585C>A	ENST00000498297.1	-	0	868				RP11-723O4.9_ENST00000567253.1_lincRNA|RP11-723O4.2_ENST00000480931.1_RNA	NR_034179.1																						GGCACCTCCACGGCAGAAATG	0.587													C|||	1641	0.327676	0.3525	0.2695	5008	,	,		20008	0.5645		0.1879	False		,,,				2504	0.2352				.													.	.			0			.																																											0	.			CCTCCACGGCAGA																													3.37:g.128580585C>A			151	0	0		158	0.05	8	.	7	0.00	0		RNA	SNP	ENST00000498297.1	37																																																																																						0.587	RP11-723O4.2-001	KNOWN	basic	antisense	antisense		OTTHUMT00000357491.1			
Unknown	0	bcgsc.ca	37	3	132105901	132105901	+	IGR	SNP	A	A	G	rs2124506	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:132105901A>G								ACPP (18759 upstream) : DNAJC13 (30468 downstream)																							CCATTTGCTCAGAATTTATTG	0.333													G|||	1392	0.277955	0.2012	0.2046	5008	,	,		20384	0.5317		0.1819	False		,,,				2504	0.271				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTGCTCAGAATTT																													3.37:g.132105901A>G			108	0	0		102	0.08	8	.	0		0		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	3	166579857	166579857	+	IGR	SNP	C	C	T	rs9832877	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:166579857C>T								RP11-12K11.2 (17113 upstream) : AC092965.1 (163343 downstream)																							GTAATCTGTACTTTTGTATGT	0.328													T|||	3516	0.702077	0.8669	0.7262	5008	,	,		12783	0.3175		0.8062	False		,,,				2504	0.7515				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGTACTTTTGT																													3.37:g.166579857C>T			131	0.0152671756	2		131	0.12	16	.	0		0		RNA	SNP		37																																																																																					0	0.328										
PSMD10P2	280644	bcgsc.ca	37	3	186479009	186479009	+	RNA	SNP	A	A	G	rs866601	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr3:186479009A>G	ENST00000596329.1	-	0	0				RP11-573D15.8_ENST00000608173.1_RNA																							CTAGAACAGCAGAACTGCATT	0.468													A|||	3749	0.748602	0.8018	0.5951	5008	,	,		18799	0.8413		0.6561	False		,,,				2504	0.7853				.													.	.			0			.																																											280644	.			AACAGCAGAACTG																													3.37:g.186479009A>G			103	0	0		139	0.06	9	.	1	0.00	0		RNA	SNP	ENST00000596329.1	37																																																																																						0.468	RP11-573D15.8-002	KNOWN	basic	antisense	antisense		OTTHUMT00000461601.1			
ALG1L7P	728263	bcgsc.ca	37	4	3938121	3938121	+	IGR	SNP	C	C	T	rs7676401	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:3938121C>T								ADRA2C (167870 upstream) : FAM86EP (5365 downstream)																							GCGGCCAGCCCTGCTGGTCAG	0.632													.|||	1752	0.34984	0.3177	0.3069	5008	,	,		17091	0.4921		0.2843	False		,,,				2504	0.3446				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAGCCCTGCTGG																													4.37:g.3938121C>T			90	0	0		63	0.08	5	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.632										
GMPSP1	728564	bcgsc.ca	37	4	8176480	8176480	+	IGR	SNP	G	G	A	rs11547949	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:8176480G>A								ABLIM2 (15921 upstream) : SH3TC1 (24610 downstream)																							GCCAGATGCCGGTGATTTTGA	0.463													G|||	281	0.0561102	0.177	0.0375	5008	,	,		18364	0.0		0.0179	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001628	intergenic_variant	728564	.			GATGCCGGTGATT																													4.37:g.8176480G>A			138	0	0		94	0.06	6	.	114	0.00	0		RNA	SNP		37																																																																																					0	0.463										
OR7E85P	442105	bcgsc.ca	37	4	9486098	9486098	+	IGR	SNP	C	C	G	rs114281488	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:9486098C>G								AC116655.1 (13314 upstream) : MIR548I2 (71690 downstream)																							CTCTGGATTTCATCTTCAGAT	0.398													.|||	662	0.132188	0.174	0.2118	5008	,	,		23203	0.0456		0.1223	False		,,,				2504	0.1186				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGATTTCATCTTC																													4.37:g.9486098C>G			236	0	0		170	0.04	6	.	0		0		RNA	SNP		37																																																																																					0	0.398										
ALG1L3P	100132066	bcgsc.ca	37	4	9711554	9711554	+	IGR	SNP	G	G	A	rs111695399	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:9711554G>A								AC097493.1 (109503 upstream) : DRD5 (71703 downstream)																							AAGGCCGACCGCTCCGTGGCT	0.612													.|||	107	0.0213658	0.0711	0.0187	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCGACCGCTCCGT																													4.37:g.9711554G>A			159	0.0062893082	1		126	0.05	6	.	0		0		RNA	SNP		37																																																																																					0	0.612										
MESTP3	645641	bcgsc.ca	37	4	28825584	28825584	+	IGR	SNP	G	G	A	rs12644777	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:28825584G>A								RN7SL101P (112490 upstream) : RP11-292B1.2 (172561 downstream)																							TGTACCAATCGTAGCTGGATG	0.453													G|||	1767	0.352835	0.0325	0.4251	5008	,	,		20543	0.8075		0.2485	False		,,,				2504	0.3732				.													.	.			0			.																																									SO:0001628	intergenic_variant	645641	.			CCAATCGTAGCTG																													4.37:g.28825584G>A			46	0	0		31	0.16	5	.	6	0.00	0		RNA	SNP		37																																																																																					0	0.453										
Unknown	0	bcgsc.ca	37	4	33012957	33012957	+	IGR	SNP	A	A	G	rs6531315	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:33012957A>G								RP11-240A16.1 (658115 upstream) : RP11-802H3.2 (422174 downstream)																							AGCCACTGCAATTTCTTGACC	0.458													.|||	969	0.19349	0.5083	0.1326	5008	,	,		17561	0.005		0.1272	False		,,,				2504	0.0736				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACTGCAATTTCTT																													4.37:g.33012957A>G			63	0	0		47	0.09	4	.	0		0		RNA	SNP		37																																																																																					0	0.458										
Unknown	0	bcgsc.ca	37	4	49244932	49244932	+	IGR	SNP	C	C	T	rs201474862		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:49244932C>T								AC118282.4 (33467 upstream) : AC119751.5 (340109 downstream)																							CTGATCATTGCTATTTTCTTA	0.353																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCATTGCTATTTT																													4.37:g.49244932C>T			19	0	0		15	0.33	5	.	0		0		RNA	SNP		37																																																																																					0	0.353										
Unknown	0	bcgsc.ca	37	4	57627451	57627451	+	IGR	SNP	G	G	A	rs2016218	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:57627451G>A								HOPX (79386 upstream) : RN7SL492P (33064 downstream)																							CATGTCCTTTGGAAAGCCATT	0.398													A|||	1771	0.353634	0.6967	0.2767	5008	,	,		20024	0.2272		0.2147	False		,,,				2504	0.2178				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCCTTTGGAAAGC																													4.37:g.57627451G>A			172	0.011627907	2		103	0.10	10	.	0		0		RNA	SNP		37																																																																																					0	0.398										
EXOC5P1	644548	bcgsc.ca	37	4	63683674	63683674	+	IGR	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:63683674G>A								AC110810.1 (222494 upstream) : RP11-257A22.1 (310354 downstream)																							TTTGAAAGATGTCATAGGCTC	0.383																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			AAAGATGTCATAG																													4.37:g.63683674G>A			138	0	0		65	0.32	21	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.383										
Unknown	0	bcgsc.ca	37	4	70212704	70212704	+	IGR	SNP	G	G	A	rs6851810	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:70212704G>A								UGT2B28 (51936 upstream) : AC108078.1 (132344 downstream)																							TGATGTTTGAGAGCATTATCT	0.398													N|||	1630	0.325479	0.3154	0.3343	5008	,	,		14396	0.372		0.2903	False		,,,				2504	0.3211				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTTGAGAGCATT																													4.37:g.70212704G>A			98	0	0		57	0.12	7	.	0		0		RNA	SNP		37																																																																																					0	0.398										
BIN2P1	345258	bcgsc.ca	37	4	83196536	83196536	+	IGR	SNP	G	G	A	rs13119500	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:83196536G>A								RNU6-499P (100730 upstream) : RP11-127B20.2 (69492 downstream)																							AGAATGCCAAGAAAGATGAGG	0.488													G|||	771	0.153954	0.2973	0.0807	5008	,	,		20884	0.125		0.1233	False		,,,				2504	0.0736				.													.	.			0			.																																									SO:0001628	intergenic_variant	345258	.			TGCCAAGAAAGAT																													4.37:g.83196536G>A			29	0	0		24	0.21	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.488										
IGBP1P4	391672	bcgsc.ca	37	4	83323062	83323062	+	RNA	SNP	T	T	C	rs7695741	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:83323062T>C	ENST00000365570.1	-	0	69																											GAGTTAGAAGTTGATGCCTCC	0.458													T|||	584	0.116613	0.1543	0.1167	5008	,	,		19588	0.0724		0.1581	False		,,,				2504	0.0685				.													.	.			0			.																																											391672	.			TAGAAGTTGATGC																													4.37:g.83323062T>C			115	0	0		81	0.10	8	.	0		0		RNA	SNP	ENST00000365570.1	37																																																																																						0.458	SNORD42.2-201	NOVEL	basic	snoRNA	snoRNA					
SEC31A	22872	ucsc.edu	37	4	83778879	83778879	+	Silent	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:83778879G>T	ENST00000395310.2	-	15	1847	c.1665C>A	c.(1663-1665)ccC>ccA	p.P555P	SEC31A_ENST00000448323.1_Silent_p.P555P|SEC31A_ENST00000264405.5_Silent_p.P288P|SEC31A_ENST00000508502.1_Silent_p.P555P|SEC31A_ENST00000513858.1_Silent_p.P516P|SEC31A_ENST00000508479.1_Silent_p.P555P|SEC31A_ENST00000326950.5_Silent_p.P516P|SEC31A_ENST00000509142.1_Silent_p.P555P|SEC31A_ENST00000505984.1_Silent_p.P516P|SEC31A_ENST00000355196.2_Silent_p.P555P|SEC31A_ENST00000348405.4_Silent_p.P516P|SEC31A_ENST00000443462.2_Silent_p.P550P|SEC31A_ENST00000505472.1_Silent_p.P555P|SEC31A_ENST00000311785.7_Silent_p.P555P|SEC31A_ENST00000500777.2_Silent_p.P516P|SEC31A_ENST00000432794.1_Silent_p.P555P	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	555					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				CTCCAGATGAGGGTAGAAATT	0.328																																					p.P555P													.	SEC31A	227		0			c.C1665A												121.0	127.0	125.0					4																	83778879		2203	4300	6503	SO:0001819	synonymous_variant	22872	exon15			AGATGAGGGTAGA	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.1665C>A	4.37:g.83778879G>T			53	0	0		43	0.09	4	NM_001077206	181	0.00	0	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	G	0.960	-0.703461	0.03255	.	.	ENSG00000138674	ENST00000507828;ENST00000512664	.	.	.	5.85	-2.68	0.06041	.	.	.	.	.	T	0.21801	0.0525	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.31752	-0.9932	4	.	.	.	-4.4254	4.7914	0.13250	0.1351:0.0684:0.3415:0.455	.	.	.	.	I	172;70	.	.	L	-	1	0	SEC31A	83997903	0.000000	0.05858	0.184000	0.23157	0.298000	0.27526	-2.318000	0.01121	-0.214000	0.10078	-0.169000	0.13324	CTC			0.328	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000252640.1		NM_016211	
LYPLA1P2	391686	bcgsc.ca	37	4	111866561	111866561	+	IGR	SNP	C	C	T	rs28696178	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:111866561C>T								MIR297 (84758 upstream) : RNU6-289P (386006 downstream)																							GTTTCTGCTACGTGGTAAGGG	0.463													C|||	316	0.063099	0.2224	0.0288	5008	,	,		17089	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	391686	.			CTGCTACGTGGTA																													4.37:g.111866561C>T			62	0	0		36	0.11	4	.	0		0		RNA	SNP		37																																																																																					0	0.463										
KLHL2P1	729249	bcgsc.ca	37	4	120275268	120275268	+	IGR	SNP	A	A	G	rs62320725	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120275268A>G								FABP2 (31723 upstream) : RNU4-33P (13448 downstream)																							GTTTTAGGTGAGATGAGTGAG	0.428													A|||	529	0.105631	0.1634	0.0764	5008	,	,		19253	0.0427		0.1362	False		,,,				2504	0.0818				.													.	.			0			.																																									SO:0001628	intergenic_variant	729249	.			TAGGTGAGATGAG																													4.37:g.120275268A>G			284	0	0		213	0.08	17	.	0		0		RNA	SNP		37																																																																																					0	0.428										
Unknown	0	bcgsc.ca	37	4	120314664	120314664	+	IGR	SNP	T	T	C	rs13127114	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120314664T>C								RNU4-33P (25863 upstream) : RP11-33B1.4 (15823 downstream)																							ACCGCTCCATTGTGACGGCGG	0.498													.|||	1412	0.281949	0.2791	0.2839	5008	,	,		17488	0.3879		0.2833	False		,,,				2504	0.1738				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCCATTGTGACG																													4.37:g.120314664T>C			171	0	0		104	0.11	11	.	0		0		RNA	SNP		37																																																																																					0	0.498										
Unknown	0	bcgsc.ca	37	4	120314741	120314741	+	IGR	SNP	C	C	A	rs13151285	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120314741C>A								RNU4-33P (25940 upstream) : RP11-33B1.4 (15746 downstream)																							ATGGCAGCACCCAATGCAGTG	0.512													.|||	1411	0.281749	0.2784	0.2839	5008	,	,		18136	0.3879		0.2833	False		,,,				2504	0.1738				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGCACCCAATGC																													4.37:g.120314741C>A			184	0	0		98	0.08	8	.	0		0		RNA	SNP		37																																																																																					0	0.512										
Unknown	0	bcgsc.ca	37	4	120314881	120314881	+	IGR	SNP	A	A	G	rs4309825	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120314881A>G								RNU4-33P (26080 upstream) : RP11-33B1.4 (15606 downstream)																							GTCTCAATTCATGGCATCCAA	0.398													.|||	1410	0.28155	0.2784	0.2839	5008	,	,		20413	0.3879		0.2833	False		,,,				2504	0.1728				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAATTCATGGCAT																													4.37:g.120314881A>G			343	0	0		240	0.07	16	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	4	120314921	120314921	+	IGR	SNP	C	C	T	rs4604043	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120314921C>T								RNU4-33P (26120 upstream) : RP11-33B1.4 (15566 downstream)																							CAAACAGCTTCTAATGCAGCA	0.438													.|||	1411	0.281749	0.2784	0.2839	5008	,	,		19692	0.3879		0.2833	False		,,,				2504	0.1738				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGCTTCTAATGC																													4.37:g.120314921C>T			359	0	0		258	0.07	18	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.438										
Unknown	0	bcgsc.ca	37	4	120315906	120315906	+	IGR	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120315906C>T								RNU4-33P (27105 upstream) : RP11-33B1.4 (14581 downstream)																							CACATGTTTTCGCTATACACT	0.408																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTTTTCGCTATA																													4.37:g.120315906C>T			204	0	0		176	0.06	10	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.408										
Unknown	0	bcgsc.ca	37	4	120316075	120316075	+	IGR	SNP	A	A	G	rs11098513	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:120316075A>G								RNU4-33P (27274 upstream) : RP11-33B1.4 (14412 downstream)																							CACTGCCCCCACCAATGGCCC	0.542													.|||	1426	0.284744	0.289	0.2853	5008	,	,		15993	0.3879		0.2823	False		,,,				2504	0.1748				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCCCCCACCAATG																													4.37:g.120316075A>G			150	0.0133333333	2		135	0.07	10	.	0		0		RNA	SNP		37																																																																																					0	0.542										
RP11-679C8.2	0	bcgsc.ca	37	4	121263497	121263497	+	RNA	SNP	G	G	A	rs1160185	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:121263497G>A	ENST00000508362.1	+	0	286				RP11-679C8.2_ENST00000504106.1_RNA																							AATGAATGGGGTTATCTTTCT	0.383													A|||	3480	0.694888	0.7133	0.6066	5008	,	,		19931	0.7589		0.7008	False		,,,				2504	0.6605				.													.	.			0			.																																											344988	.			AATGGGGTTATCT																													4.37:g.121263497G>A			22	0	0		16	0.31	5	.	0		0		RNA	SNP	ENST00000508362.1	37																																																																																						0.383	RP11-679C8.2-001	KNOWN	basic	antisense	antisense		OTTHUMT00000363869.2			
RANP6	100128266	bcgsc.ca	37	4	174555444	174555444	+	IGR	SNP	C	C	T	rs60395447	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:174555444C>T								RP11-475B2.1 (39737 upstream) : RP11-161D15.2 (262100 downstream)																							TGATGTTTCACGAAGGTCGTT	0.468													C|||	2676	0.534345	0.4153	0.6239	5008	,	,		19354	0.6617		0.5596	False		,,,				2504	0.4744				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128266	.			GTTTCACGAAGGT																													4.37:g.174555444C>T			64	0	0		28	0.18	5	.	0		0		RNA	SNP		37																																																																																					0	0.468										
Unknown	0	bcgsc.ca	37	4	189660460	189660460	+	IGR	SNP	G	G	C	rs60608362	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:189660460G>C								RNU7-192P (22581 upstream) : RP11-756P10.4 (18372 downstream)																							TGGAAGTAAAGGAAGATCAGA	0.358													-|||	356	0.0710863	0.1256	0.0476	5008	,	,		19100	0.0595		0.0408	False		,,,				2504	0.0573				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTAAAGGAAGAT																													4.37:g.189660460G>C			205	0	0		120	0.06	7	.	30	0.00	0		RNA	SNP		37																																																																																					0	0.358										
HSP90AA4P	3323	bcgsc.ca	37	4	190395259	190395259	+	RNA	SNP	C	C	G	rs13143685	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr4:190395259C>G	ENST00000378770.1	+	0	539							Q58FG1	HS904_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 4, pseudogene						protein folding (GO:0006457)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)										CTGTGAGGAGCTAATCCCTGA	0.418													C|||	409	0.0816693	0.0234	0.111	5008	,	,		18549	0.001		0.2068	False		,,,				2504	0.0941				.													.	.			0			.																																											3323	.			GAGGAGCTAATCC			4q35.2	2011-04-15	2011-04-15	2006-02-24	ENSG00000205100	ENSG00000205100			5255	pseudogene	pseudogene			"""heat shock 90kD protein 1, alpha-like 2"", ""heat shock 90kDa protein 1, alpha-like 2"""	HSPCAL2		1740332, 16269234	Standard	NG_003014		Approved			Q58FG1	OTTHUMG00000160204		4.37:g.190395259C>G			94	0	0		54	0.13	7	.	0		0		RNA	SNP	ENST00000378770.1	37																																																																																						0.418	HSP90AA4P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000359634.1		NG_003014	
ZDHHC11B	653082	bcgsc.ca	37	5	766939	766939	+	Silent	SNP	G	G	A	rs4957103	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:766939G>A	ENST00000382776.4	-	1	95	c.96C>T	c.(94-96)aaC>aaT	p.N32N	ZDHHC11_ENST00000424784.2_Intron|ZDHHC11B_ENST00000508859.2_Silent_p.N43N			P0C7U3	ZH11B_HUMAN	zinc finger, DHHC-type containing 11B	32						integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			lung(3)|stomach(1)	4						ACGACCAGCCGTTCACTCTGG	0.597																																					.													ZDHHC11B,NS,carcinoma,0,1	.		1	0			.																																									SO:0001819	synonymous_variant	653082	.			CCAGCCGTTCACT			5p15.33	2007-01-29				ENSG00000206077		"""Zinc fingers, DHHC-type"""	32962	protein-coding gene	gene with protein product							Standard	XM_003118532		Approved			P0C7U3		ENST00000382776.4:c.96C>T	5.37:g.766939G>A			76	0	0		61	0.08	5	.	0		0	A6NHR3	Silent	SNP	ENST00000382776.4	37																																																																																						0.597	ZDHHC11B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				XM_926053	
ZDHHC11	79844	bcgsc.ca	37	5	843766	843766	+	Missense_Mutation	SNP	C	C	T	rs76685897	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:843766C>T	ENST00000283441.8	-	4	960	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.V193I|ZDHHC11_ENST00000511539.1_5'UTR|ZDHHC11_ENST00000503758.2_5'Flank	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	193						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			AGGTACTGGACGAGGACATAC	0.642													c|||	399	0.0796725	0.1649	0.0288	5008	,	,		16612	0.128		0.0099	False		,,,				2504	0.0225				p.V193I													.	ZDHHC11	97		0			c.G577A												72.0	56.0	61.0					5																	843766		2201	4287	6488	SO:0001583	missense	79844	exon4			ACTGGACGAGGAC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.577G>A	5.37:g.843766C>T	ENSP00000283441:p.Val193Ile		511	0	0		341	0.04	15	NM_024786	7	0.00	0	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	143	0.06547619047619048	68	0.13821138211382114	7	0.019337016574585635	63	0.11013986013986014	5	0.006596306068601583	c	7.287	0.610316	0.14066	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.23147	1.92;1.92	3.98	-3.06	0.05379	.	1.820040	0.04629	U	0.403297	T	0.00073	0.0002	N	0.02120	-0.675	0.09310	N	1	B	0.23442	0.085	B	0.31495	0.131	T	0.13442	-1.0509	10	0.02654	T	1	-3.8682	4.1404	0.10191	0.2887:0.1162:0.0:0.595	.	193	Q9H8X9	ZDH11_HUMAN	I	193	ENSP00000397719:V193I;ENSP00000283441:V193I	ENSP00000283441:V193I	V	-	1	0	ZDHHC11	896766	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-1.014000	0.03379	-0.561000	0.04177	GTC			0.642	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206681.3		NM_024786	
CCT6P2	391739	bcgsc.ca	37	5	14639939	14639939	+	IGR	SNP	C	C	T	rs144306780	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:14639939C>T								FAM105A (24823 upstream) : CTD-2165H16.4 (21977 downstream)																							TTTTTGACAGCCCTCAAGCCA	0.433													C|||	58	0.0115815	0.0008	0.0058	5008	,	,		19838	0.001		0.0129	False		,,,				2504	0.0399				.													.	.			0			.																																									SO:0001628	intergenic_variant	391739	.			TGACAGCCCTCAA																													5.37:g.14639939C>T			58	0	0		31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.433										
MSNP1	4479	bcgsc.ca	37	5	25909764	25909764	+	IGR	SNP	C	C	T	rs11739167	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:25909764C>T								RNU6-374P (208331 upstream) : RNU4-43P (103233 downstream)																							AGTACCAGGACACCAAAGGTT	0.498													C|||	2669	0.532947	0.6241	0.4395	5008	,	,		18153	0.6101		0.4205	False		,,,				2504	0.5123				.													.	.			0			.																																									SO:0001628	intergenic_variant	4479	.			CCAGGACACCAAA																													5.37:g.25909764C>T			116	0	0		64	0.14	9	.	32	0.00	0		RNA	SNP		37																																																																																					0	0.498										
MSNP1	4479	bcgsc.ca	37	5	25910566	25910566	+	IGR	SNP	A	A	G	rs12655221	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:25910566A>G								RNU6-374P (209133 upstream) : RNU4-43P (102431 downstream)																							CACCAGAAGCAGATGGAGCGT	0.542													A|||	1383	0.276158	0.1271	0.2291	5008	,	,		18177	0.3522		0.3141	False		,,,				2504	0.3937				.													.	.			0			.																																									SO:0001628	intergenic_variant	4479	.			AGAAGCAGATGGA																													5.37:g.25910566A>G			191	0	0		102	0.25	26	.	23	0.00	0		RNA	SNP		37																																																																																					0	0.542										
MSNP1	4479	bcgsc.ca	37	5	25911136	25911136	+	IGR	SNP	C	C	A	rs9293194	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:25911136C>A								RNU6-374P (209703 upstream) : RNU4-43P (101861 downstream)																							GAGGAATGTACCACTGAGGCA	0.567													C|||	2570	0.513179	0.5446	0.4337	5008	,	,		19901	0.6121		0.4205	False		,,,				2504	0.5204				.													.	.			0			.																																									SO:0001628	intergenic_variant	4479	.			AATGTACCACTGA																													5.37:g.25911136C>A			237	0.0042194093	1		163	0.16	26	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.567										
Unknown	0	bcgsc.ca	37	5	32523748	32523748	+	IGR	SNP	T	T	C	rs591985	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:32523748T>C								ZFR (78881 upstream) : SUB1 (8175 downstream)																							CACCCTCAATTTCATCTTCAT	0.463													T|||	1101	0.219848	0.2216	0.2133	5008	,	,		22078	0.3105		0.1521	False		,,,				2504	0.1984				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCAATTTCATCT																													5.37:g.32523748T>C			222	0.0045045045	1		162	0.05	8	.	0		0		RNA	SNP		37																																																																																					0	0.463										
INTS6P1	285634	bcgsc.ca	37	5	39719446	39719446	+	IGR	SNP	A	A	G	rs10512714	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:39719446A>G								CTD-2078B5.2 (194636 upstream) : LINC00603 (332946 downstream)																							AAAATCCACCAACAGTGAGGT	0.413													A|||	1257	0.250998	0.1649	0.2161	5008	,	,		18916	0.1716		0.3559	False		,,,				2504	0.3661				.													.	.			0			.																																									SO:0001628	intergenic_variant	285634	.			TCCACCAACAGTG																													5.37:g.39719446A>G			72	0	0		53	0.15	8	.	0		0		RNA	SNP		37																																																																																					0	0.413										
Unknown	0	bcgsc.ca	37	5	41586211	41586211	+	IGR	SNP	T	T	G	rs634858	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:41586211T>G								PLCXD3 (75481 upstream) : OXCT1 (143955 downstream)																							AGATTTTTACTTTCTGGGTTA	0.383																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTACTTTCTGG																													5.37:g.41586211T>G			24	0	0		16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.383										
Unknown	0	bcgsc.ca	37	5	41587666	41587666	+	IGR	SNP	C	C	T	rs661845	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:41587666C>T								PLCXD3 (76936 upstream) : OXCT1 (142500 downstream)																							CAAAGAACTTCAGCTGCAGGA	0.438													T|||	837	0.167133	0.3169	0.1686	5008	,	,		20680	0.0069		0.162	False		,,,				2504	0.1339				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAACTTCAGCTGC																													5.37:g.41587666C>T			75	0	0		57	0.14	8	.	0		0		RNA	SNP		37																																																																																					0	0.438										
Unknown	0	bcgsc.ca	37	5	41587802	41587802	+	IGR	SNP	T	T	C	rs79920342	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:41587802T>C								PLCXD3 (77072 upstream) : OXCT1 (142364 downstream)																							GTATTGGCAATTGAAGCTTAA	0.502													T|||	279	0.0557109	0.0651	0.0692	5008	,	,		20173	0.001		0.0845	False		,,,				2504	0.0603				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGCAATTGAAGC																													5.37:g.41587802T>C			48	0	0		33	0.12	4	.	0		0		RNA	SNP		37																																																																																					0	0.502										
FBXO4	26272	hgsc.bcm.edu;bcgsc.ca	37	5	41927269	41927269	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:41927269G>T	ENST00000281623.3	+	2	400	c.344G>T	c.(343-345)tGg>tTg	p.W115L	FBXO4_ENST00000509134.1_Missense_Mutation_p.W115L|FBXO4_ENST00000296812.2_Missense_Mutation_p.W115L	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	115					positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|telomere maintenance (GO:0000723)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(11)|prostate(1)|stomach(1)|urinary_tract(2)	27		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)				TCTGTTGACTGGAAGTCTCTT	0.368																																					p.W115L													.	.			0			c.G344T												157.0	157.0	157.0					5																	41927269		2203	4300	6503	SO:0001583	missense	26272	exon2			TTGACTGGAAGTC	AF129534	CCDS3938.1, CCDS3939.1, CCDS75238.1	5p12	2008-02-05	2004-06-15		ENSG00000151876	ENSG00000151876		"""F-boxes /  ""other"""""	13583	protein-coding gene	gene with protein product		609090	"""F-box only protein 4"""			10531035, 10531037	Standard	NM_033484		Approved	FBX4	uc003jmq.3	Q9UKT5	OTTHUMG00000094799	ENST00000281623.3:c.344G>T	5.37:g.41927269G>T	ENSP00000281623:p.Trp115Leu		191	0	0		120	0.05	6	NM_033484	28	0.00	0	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	37	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.090937	0.76756	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.51325	0.71;0.71;0.71	5.62	5.62	0.85841	F-box domain, Skp2-like (1);	0.126462	0.64402	D	0.000009	T	0.60702	0.2289	L	0.51422	1.61	0.52501	D	0.999958	P;D;D	0.63880	0.956;0.993;0.991	P;P;P	0.57101	0.549;0.813;0.647	T	0.60601	-0.7231	10	0.56958	D	0.05	-10.1697	19.6604	0.95864	0.0:0.0:1.0:0.0	.	115;115;115	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	L	115	ENSP00000296812:W115L;ENSP00000281623:W115L;ENSP00000421749:W115L	ENSP00000281623:W115L	W	+	2	0	FBXO4	41963026	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.601000	0.74136	2.648000	0.89879	0.655000	0.94253	TGG			0.368	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000211614.1			
GLRX	2745	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	95152294	95152294	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:95152294C>T	ENST00000379979.4	-	2	295	c.244G>A	c.(244-246)Gga>Aga	p.G82R	GLRX_ENST00000505427.1_Missense_Mutation_p.G82R|GLRX_ENST00000512469.2_Missense_Mutation_p.G82R|GLRX_ENST00000507605.1_5'UTR|GLRX_ENST00000508780.1_Missense_Mutation_p.G82R|GLRX_ENST00000237858.6_Missense_Mutation_p.G82R	NM_002064.2	NP_002055.1	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)	82	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of membrane potential (GO:0045838)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein deglutathionylation (GO:0080058)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|glutathione oxidoreductase activity (GO:0097573)|protein N-terminus binding (GO:0047485)			endometrium(3)|large_intestine(1)|lung(1)	5		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	TCACTGCATCCGCCTATACAA	0.463																																					p.G82R													GLRX,NS,carcinoma,0,1	GLRX	0	1	0			c.G244A												82.0	77.0	79.0					5																	95152294		2203	4300	6503	SO:0001583	missense	2745	exon2			TGCATCCGCCTAT		CCDS4078.1	5q14	2008-02-05			ENSG00000173221	ENSG00000173221			4330	protein-coding gene	gene with protein product		600443				8838810	Standard	NM_002064		Approved	GRX, GRX1	uc021ybo.1	P35754	OTTHUMG00000121167	ENST00000379979.4:c.244G>A	5.37:g.95152294C>T	ENSP00000369314:p.Gly82Arg		123	0	0		83	0.12	10	NM_001243659	100	0.07	7	B2R4L2|Q3KQS1|Q6ICT1	Missense_Mutation	SNP	ENST00000379979.4	37	CCDS4078.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.426843	0.62733	.	.	ENSG00000173221	ENST00000508780;ENST00000237858;ENST00000379979;ENST00000505427;ENST00000512469	T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61	4.97	3.2	0.36748	Glutaredoxin subgroup (1);Glutaredoxin (1);Glutaredoxin, eukaryotic/virial (1);Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.53514	0.1801	M	0.93939	3.475	0.80722	D	1	P	0.44090	0.826	B	0.38378	0.272	T	0.60362	-0.7278	10	0.66056	D	0.02	-36.9291	7.3415	0.26640	0.0:0.8041:0.0:0.1959	.	82	P35754	GLRX1_HUMAN	R	82	ENSP00000422708:G82R;ENSP00000237858:G82R;ENSP00000369314:G82R;ENSP00000427353:G82R;ENSP00000424636:G82R	ENSP00000237858:G82R	G	-	1	0	GLRX	95178050	0.989000	0.36119	0.395000	0.26283	0.416000	0.31233	5.100000	0.64560	0.699000	0.31761	0.561000	0.74099	GGA			0.463	GLRX-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000370267.1		NM_002064	
PCDHB4	56131	ucsc.edu;bcgsc.ca	37	5	140502343	140502344	+	Missense_Mutation	DNP	CC	CC	TT	rs3733697|rs3733698|rs377479392	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr5:140502343_140502344CC>TT	ENST00000194152.1	+	1	763_764	c.763_764CC>TT	c.(763-765)CCc>TTc	p.P255F	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	255	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in dbSNP:rs3733697).|P -> S (in dbSNP:rs3733698).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAAAACAGCCCCCTAGACTCT	0.455																																					p.P255F													.	PCDHB4	177		0			c.C764T																																									SO:0001583	missense	56131	exon1			AACAGCCCCCTAG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	Exception_encountered	5.37:g.140502343_140502344delinsTT	ENSP00000194152:p.Pro255Phe		187	0	0		102	0.15	15	NM_018938	1	0.00	0	Q4V761	Missense_Mutation	DNP	ENST00000194152.1	37	CCDS4246.1																																																																																					0.455	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251812.2		NM_018938	
Unknown	0	bcgsc.ca	37	6	1514247	1514247	+	IGR	SNP	G	G	A	rs12211247	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:1514247G>A								RN7SL352P (6396 upstream) : RP11-157J24.2 (14351 downstream)																							ACAGCCAATGGAGCTCCAACA	0.512													G|||	504	0.100639	0.0129	0.1686	5008	,	,		20613	0.001		0.2793	False		,,,				2504	0.09				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAATGGAGCTCC																													6.37:g.1514247G>A			18	0	0		16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.512										
Unknown	0	bcgsc.ca	37	6	1514652	1514652	+	IGR	SNP	C	C	T	rs3902814	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:1514652C>T								RN7SL352P (6801 upstream) : RP11-157J24.2 (13946 downstream)																							TAGCCACACCCTTCTCTGCTC	0.473													C|||	526	0.105032	0.0212	0.1686	5008	,	,		21459	0.001		0.2793	False		,,,				2504	0.1012				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACACCCTTCTCT																													6.37:g.1514652C>T			51	0	0		31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.473										
CDYL	9425	bcgsc.ca;mdanderson.org	37	6	4716016	4716016	+	Missense_Mutation	SNP	A	A	G	rs3812179	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:4716016A>G	ENST00000328908.5	+	2	135	c.4A>G	c.(4-6)Aca>Gca	p.T2A				Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	2			T -> A (in dbSNP:rs3812179). {ECO:0000269|PubMed:10192397}.		regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.T2A(2)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		GAATTTTATGACATTTCAGGC	0.463													G|||	1178	0.235224	0.3116	0.3256	5008	,	,		14327	0.2679		0.2247	False		,,,				2504	0.045				.													CDYL,NS,carcinoma,0,2	.		2	2	Substitution - Missense(2)	stomach(1)|lung(1)	.							G		1238,3168	702.8+/-406.9	183,872,1148	50.0	54.0	53.0			2.9	0.6	6	dbSNP_107	53	1808,6792	730.6+/-406.8	197,1414,2689	no	intergenic				380,2286,3837	GG,GA,AA		21.0233,28.098,23.42			4716016	3046,9960	2203	4300	6503	SO:0001583	missense	9425	.			TTTATGACATTTC	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.4A>G	6.37:g.4716016A>G	ENSP00000330512:p.Thr2Ala		262	0.0038167939	1		229	0.06	14	.	0		0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		560	0.2564102564102564	148	0.3008130081300813	106	0.292817679558011	140	0.24475524475524477	166	0.21899736147757257	G	0.006	-2.024730	0.00414	0.28098	0.210233	ENSG00000153046	ENST00000328908	T	0.45276	0.9	5.79	2.87	0.33458	.	.	.	.	.	T	0.04182	0.0116	.	.	.	0.51767	P	6.499999999998174E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	7	0.02654	T	1	.	2.3124	0.04190	0.1653:0.1514:0.5267:0.1565	rs3812179;rs60069724;rs3812179	2	Q9Y232	CDYL1_HUMAN	A	2	ENSP00000330512:T2A	ENSP00000330512:T2A	T	+	1	0	CDYL	4661015	0.003000	0.15002	0.563000	0.28383	0.003000	0.03518	0.791000	0.26915	0.362000	0.24319	-0.128000	0.14901	ACA			0.463	CDYL-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000039736.1		NM_004824	
CDYL	9425	bcgsc.ca	37	6	4716037	4716037	+	Missense_Mutation	SNP	T	T	C	rs3812178	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:4716037T>C	ENST00000328908.5	+	2	156	c.25T>C	c.(25-27)Tca>Cca	p.S9P				Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	9			S -> P (in dbSNP:rs3812178). {ECO:0000269|PubMed:10192397}.		regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.S9P(2)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AAGCCACAGGTCAGCCTGGGG	0.448													C|||	1178	0.235224	0.3116	0.3256	5008	,	,		15162	0.2679		0.2247	False		,,,				2504	0.045				.													CDYL,NS,carcinoma,0,2	.		2	2	Substitution - Missense(2)	stomach(1)|lung(1)	.							C		1239,3167	704.2+/-407.1	184,871,1148	62.0	66.0	65.0			3.3	0.0	6	dbSNP_107	65	1807,6793	732.1+/-406.8	196,1415,2689	no	intergenic				380,2286,3837	CC,CT,TT		21.0116,28.1207,23.42			4716037	3046,9960	2203	4300	6503	SO:0001583	missense	9425	.			CACAGGTCAGCCT	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.25T>C	6.37:g.4716037T>C	ENSP00000330512:p.Ser9Pro		268	0.0074626866	2		243	0.05	13	.	0		0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		560	0.2564102564102564	148	0.3008130081300813	106	0.292817679558011	140	0.24475524475524477	166	0.21899736147757257	C	0.110	-1.139865	0.01728	0.281207	0.210116	ENSG00000153046	ENST00000328908	T	0.50277	0.75	5.12	3.3	0.37823	.	.	.	.	.	T	0.12008	0.0292	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	7	0.25106	T	0.35	.	3.8314	0.08876	0.169:0.58:0.163:0.088	rs3812178;rs52807368;rs58358102;rs3812178	9	Q9Y232	CDYL1_HUMAN	P	9	ENSP00000330512:S9P	ENSP00000330512:S9P	S	+	1	0	CDYL	4661036	0.012000	0.17670	0.000000	0.03702	0.004000	0.04260	0.252000	0.18278	0.300000	0.22699	-0.128000	0.14901	TCA			0.448	CDYL-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000039736.1		NM_004824	
CDYL	9425	bcgsc.ca	37	6	4735035	4735035	+	Missense_Mutation	SNP	T	T	C	rs13196069	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:4735035T>C	ENST00000328908.5	+	3	274	c.143T>C	c.(142-144)gTg>gCg	p.V48A				Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	48			V -> A (in dbSNP:rs13196069). {ECO:0000269|PubMed:10192397}.		regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.V48A(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AGCATCTCCGTGAGCAGTGAG	0.562													C|||	1367	0.272963	0.3056	0.3343	5008	,	,		16735	0.2946		0.2744	False		,,,				2504	0.1616				.													CDYL,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	lung(1)	.							C		1497,2909	677.6+/-403.4	267,963,973	87.0	85.0	86.0			-0.7	0.0	6	dbSNP_121	86	2274,6326	707.4+/-405.6	313,1648,2339	no	intergenic				580,2611,3312	CC,CT,TT		26.4419,33.9764,28.9943			4735035	3771,9235	2203	4300	6503	SO:0001583	missense	9425	.			TCTCCGTGAGCAG	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.143T>C	6.37:g.4735035T>C	ENSP00000330512:p.Val48Ala		89	0.0112359551	1		75	0.07	5	.	0		0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		639	0.2925824175824176	169	0.3434959349593496	122	0.3370165745856354	153	0.2674825174825175	195	0.25725593667546176	C	0.012	-1.672678	0.00758	0.339764	0.264419	ENSG00000153046	ENST00000328908	T	0.43688	0.94	1.2	-0.744	0.11101	.	.	.	.	.	T	0.04318	0.0119	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34527	-0.9825	7	0.02654	T	1	.	5.2106	0.15314	0.0:0.3945:0.0:0.6055	rs13196069;rs52792888;rs59760066;rs13196069	48	Q9Y232	CDYL1_HUMAN	A	48	ENSP00000330512:V48A	ENSP00000330512:V48A	V	+	2	0	CDYL	4680034	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.891000	0.04135	-0.839000	0.04212	-0.880000	0.02959	GTG			0.562	CDYL-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000039736.1		NM_004824	
CDYL	9425	bcgsc.ca	37	6	4735071	4735071	+	Missense_Mutation	SNP	C	C	G	rs28360500	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:4735071C>G	ENST00000328908.5	+	3	310	c.179C>G	c.(178-180)gCt>gGt	p.A60G				Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	60			A -> G (in dbSNP:rs28360500). {ECO:0000269|PubMed:10192397}.		regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)	p.A60G(1)		breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		CAGCCTCCCGCTTTACAGGTA	0.552													G|||	1326	0.264776	0.2791	0.3285	5008	,	,		16619	0.2937		0.2734	False		,,,				2504	0.1616				.													CDYL,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	lung(1)	.							G		1318,3088	697.1+/-406.2	201,916,1086	70.0	69.0	69.0			-1.9	0.0	6	dbSNP_125	69	2278,6322	707.2+/-405.6	314,1650,2336	no	intergenic				515,2566,3422	GG,GC,CC		26.4884,29.9138,27.6488			4735071	3596,9410	2203	4300	6503	SO:0001583	missense	9425	.			CTCCCGCTTTACA	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.179C>G	6.37:g.4735071C>G	ENSP00000330512:p.Ala60Gly		91	0.010989011	1		75	0.07	5	.	0		0	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		633	0.28983516483516486	158	0.32113821138211385	120	0.3314917127071823	155	0.270979020979021	200	0.2638522427440633	G	0.007	-1.995926	0.00435	0.299138	0.264884	ENSG00000153046	ENST00000328908	T	0.44083	0.93	0.923	-1.85	0.07784	Chromo domain-like (1);Chromo domain/shadow (1);	.	.	.	.	T	0.07234	0.0183	.	.	.	0.80722	P	0.0	B	0.19817	0.039	B	0.18871	0.023	T	0.29181	-1.0020	7	0.22109	T	0.4	.	3.1919	0.06620	0.3542:0.24:0.4058:0.0	rs28360500;rs57339934	60	Q9Y232	CDYL1_HUMAN	G	60	ENSP00000330512:A60G	ENSP00000330512:A60G	A	+	2	0	CDYL	4680070	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.774000	0.04684	-1.574000	0.01657	-1.394000	0.01149	GCT			0.552	CDYL-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000039736.1		NM_004824	
Unknown	0	bcgsc.ca	37	6	23972696	23972696	+	IGR	SNP	G	G	T	rs34725714	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:23972696G>T								RP11-439H9.1 (625908 upstream) : NRSN1 (153653 downstream)																							GGGCATGTTAGTTTCTTGGCT	0.493													G|||	624	0.124601	0.0749	0.1196	5008	,	,		20230	0.0675		0.161	False		,,,				2504	0.2168				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGTTAGTTTCTT																													6.37:g.23972696G>T			109	0	0		72	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.493										
HIST1H2AB	8335	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	6	26033614	26033614	+	Silent	SNP	G	G	A	rs199590202		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:26033614G>A	ENST00000259791.2	-	1	182	c.183C>T	c.(181-183)gcC>gcT	p.A61A	HIST1H3B_ENST00000244661.2_5'Flank	NM_003513.2	NP_003504.2	P04908	H2A1B_HUMAN	histone cluster 1, H2ab	61						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CCAGGATCTCGGCGGTCAGGT	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		13178	0.001		0.0	False		,,,				2504	0.0				p.A61A													.	.			0			c.C183T												40.0	43.0	42.0					6																	26033614		2203	4300	6503	SO:0001819	synonymous_variant	8335	exon1			GATCTCGGCGGTC	X00089	CCDS4574.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000137259	ENSG00000278463		"""Histones / Replication-dependent"""	4734	protein-coding gene	gene with protein product		602795	"""H2A histone family, member M"", ""histone 1, H2ab"""	H2AFM		9439656, 9119399, 12408966	Standard	NM_003513		Approved	H2A/m	uc003nft.1	P04908	OTTHUMG00000014420	ENST00000259791.2:c.183C>T	6.37:g.26033614G>A			140	0	0		102	0.17	17	NM_003513	1	1.00	1	P28001|Q76P63	Silent	SNP	ENST00000259791.2	37	CCDS4574.1																																																																																			0.001		0.662	HIST1H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040082.1		NM_003513	
HIST1H4F	8361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	26240904	26240904	+	Missense_Mutation	SNP	C	C	G	rs374666858		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:26240904C>G	ENST00000377745.2	+	1	344	c.251C>G	c.(250-252)gCa>gGa	p.A84G		NM_003540.3	NP_003531.1	P62805	H4_HUMAN	histone cluster 1, H4f	84					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				ACAGTCACTGCAATGGATGTT	0.532																																					p.A84G													.	.			0			c.C251G												97.0	81.0	87.0					6																	26240904		2203	4300	6503	SO:0001583	missense	8361	exon1			TCACTGCAATGGA	M60749	CCDS4598.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198327			"""Histones / Replication-dependent"""	4783	protein-coding gene	gene with protein product		602824	"""H4 histone family, member C"", ""histone 1, H4f"""	H4FC		1916825, 9119399, 12408966	Standard	NM_003540		Approved	H4/c, H4	uc003nhe.1	P62805	OTTHUMG00000014443	ENST00000377745.2:c.251C>G	6.37:g.26240904C>G	ENSP00000366974:p.Ala84Gly		132	0	0		98	0.22	22	NM_003540	0		0	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377745.2	37	CCDS4598.1	.	.	.	.	.	.	.	.	.	.	.	15.29	2.789341	0.49997	.	.	ENSG00000198327	ENST00000377745	T	0.69561	-0.41	4.36	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.74718	0.3753	.	.	.	0.47374	D	0.999408	.	.	.	.	.	.	T	0.78861	-0.2037	7	0.87932	D	0	.	16.4132	0.83726	0.0:1.0:0.0:0.0	.	.	.	.	G	84	ENSP00000366974:A84G	ENSP00000366974:A84G	A	+	2	0	HIST1H4F	26348883	1.000000	0.71417	0.934000	0.37439	0.118000	0.20060	7.317000	0.79018	2.430000	0.82344	0.563000	0.77884	GCA			0.532	HIST1H4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040106.1		NM_003540	
ZNF322	79692	bcgsc.ca;mdanderson.org	37	6	26637724	26637724	+	Missense_Mutation	SNP	T	T	C	rs139332558	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:26637724T>C	ENST00000415922.2	-	4	1703	c.1058A>G	c.(1057-1059)tAc>tGc	p.Y353C	ZNF322_ENST00000461899.1_5'Flank|ZNF322_ENST00000471278.1_Missense_Mutation_p.Y353C|RP11-457M11.2_ENST00000456172.1_RNA	NM_024639.4	NP_078915.2	Q6U7Q0	ZN322_HUMAN	zinc finger protein 322	353					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										ACATACAGTGTATTTATAGTG	0.428													T|||	88	0.0175719	0.0015	0.0259	5008	,	,		23200	0.0		0.0676	False		,,,				2504	0.0				p.Y353C													.	.			0			c.A1058G							T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	64,4340	50.9+/-86.3	0,64,2138	134.0	105.0	115.0		1058,1058,1058,1058	3.8	0.3	6	dbSNP_134	115	647,7943	154.5+/-208.7	16,615,3664	no	missense,missense,missense,missense	ZNF322	NM_001242797.1,NM_001242798.1,NM_001242799.1,NM_024639.4	194,194,194,194	16,679,5802	CC,CT,TT		7.532,1.4532,5.4718	probably-damaging,probably-damaging,probably-damaging,probably-damaging	353/403,353/403,353/403,353/403	26637724	711,12283	2202	4295	6497	SO:0001583	missense	79692	exon5			ACAGTGTATTTAT	AY376736	CCDS4617.1	6p22.1	2013-01-08	2011-07-29	2011-07-29	ENSG00000181315	ENSG00000181315		"""Zinc fingers, C2H2-type"""	23640	protein-coding gene	gene with protein product		610847	"""zinc finger protein 489"", ""HLA complex group 12"", ""zinc finger protein 322A"""	ZNF489, ZNF388, HCG12, ZNF322A		15555580	Standard	NM_024639		Approved	bA457M11.3, bA457M11.2	uc021yny.1	Q6U7Q0	OTTHUMG00000014460	ENST00000415922.2:c.1058A>G	6.37:g.26637724T>C	ENSP00000418897:p.Tyr353Cys		748	0.0026737968	2		633	0.04	24	NM_001242797	37	0.00	0	A8K1X3|Q0VDH6|Q6B0G2|Q86W72|Q9H5I9	Missense_Mutation	SNP	ENST00000415922.2	37	CCDS4617.1	.	.	.	.	.	.	.	.	.	.	t	0.330	-0.956764	0.02267	0.014532	0.07532	ENSG00000181315	ENST00000415922;ENST00000471278	T;T	0.04360	3.64;3.64	4.9	3.76	0.43208	.	0.000000	0.41605	D	0.000856	T	0.00210	0.0006	N	0.00008	-3.13	0.42258	D	0.992006	B	0.06786	0.001	B	0.04013	0.001	T	0.48790	-0.9004	10	0.02654	T	1	-15.2221	5.5273	0.16964	0.0:0.1858:0.0:0.8142	.	353	Q6U7Q0	ZN322_HUMAN	C	353	ENSP00000418897:Y353C;ENSP00000419728:Y353C	ENSP00000418897:Y353C	Y	-	2	0	ZNF322	26745703	0.998000	0.40836	0.261000	0.24466	0.951000	0.60555	3.629000	0.54266	2.171000	0.68590	0.533000	0.62120	TAC			0.428	ZNF322-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040126.2		NM_024639	
ZKSCAN3	80317	ucsc.edu;bcgsc.ca	37	6	28331127	28331128	+	Missense_Mutation	DNP	AA	AA	GC	rs13201752|rs13201753|rs371085669	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:28331127_28331128AA>GC	ENST00000377255.3	+	5	895_896	c.598_599AA>GC	c.(598-600)AAa>GCa	p.K200A	ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.K200A|ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.K52A	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	200			K -> A (requires 2 nucleotide substitutions; dbSNP:rs13201752). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.|K -> E (in dbSNP:rs45505399). {ECO:0000269|PubMed:14702039}.|K -> T (in dbSNP:rs13201753).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						CAGAGAAGATAAAGTGGTAGCT	0.54																																					p.K200A													ZKSCAN3,NS,other,-1,1	ZKSCAN3	50	1	0			c.A599C																																									SO:0001583	missense	80317	exon4			GAAGATAAAGTGG	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	Exception_encountered	6.37:g.28331127_28331128delinsGC	ENSP00000366465:p.Lys200Ala		101	0.0099009901	1		79	0.09	7	NM_024493	9	0.00	0	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	DNP	ENST00000377255.3	37	CCDS4650.1																																																																																					0.540	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000040189.3		NM_024493	
C6orf100	729583	bcgsc.ca;mdanderson.org	37	6	28911802	28911802	+	Splice_Site	SNP	G	G	A	rs2071790	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:28911802G>A	ENST00000377186.3	+	1	149	c.122G>A	c.(121-123)gGa>gAa	p.G41E						chromosome 6 open reading frame 100																		GGATTCCAGGGAGTAAGCCTC	0.527													A|||	3394	0.677716	0.9206	0.5793	5008	,	,		20514	0.6627		0.498	False		,,,				2504	0.6196				.													.	.			0			.																																									SO:0001630	splice_region_variant	729583	.			TCCAGGGAGTAAG			6p22.1	2011-11-25			ENSG00000204709	ENSG00000204709			21195	protein-coding gene	gene with protein product							Standard	NR_103538		Approved	dJ25J6.5		Q5JQF7	OTTHUMG00000031148	ENST00000377186.3:c.123+1G>A	6.37:g.28911802G>A			119	0	0		98	0.17	17	.	0		0		Missense_Mutation	SNP	ENST00000377186.3	37		1393	0.6378205128205128	448	0.9105691056910569	208	0.574585635359116	379	0.6625874125874126	358	0.47229551451187335	A	5.344	0.248742	0.10130	.	.	ENSG00000204709	ENST00000377186	T	0.62941	-0.01	2.9	0.945	0.19543	.	.	.	.	.	T	0.47930	0.1472	.	.	.	.	.	.	.	.	.	.	.	.	T	0.45934	-0.9227	5	0.87932	D	0	.	7.3323	0.26590	0.2589:0.0:0.7411:0.0	rs2071790;rs6456873;rs17735920;rs52814887;rs61462548;rs2071790	.	.	.	E	41	ENSP00000366391:G41E	ENSP00000366391:G41E	G	+	2	0	C6orf100	29019781	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.577000	0.02127	-0.019000	0.14055	-0.834000	0.03071	GGA			0.527	C6orf100-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000076270.1			Missense_Mutation
HLA-P	352963	bcgsc.ca	37	6	29769497	29769497	+	IGR	SNP	A	A	C	rs1610711	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:29769497A>C								HLA-V (3909 upstream) : HLA-G (25246 downstream)																							TGGTTCTTCTAGTTGCTGTAA	0.542													a|||	1163	0.232228	0.2504	0.245	5008	,	,		20405	0.1091		0.2555	False		,,,				2504	0.3016				.													.	.			0			.																																									SO:0001628	intergenic_variant	352963	.			TCTTCTAGTTGCT																													6.37:g.29769497A>C			21	0	0		27	0.22	6	.	0		0		RNA	SNP		37																																																																																					0	0.542										
HLA-G	3135	ucsc.edu	37	6	29797394	29797394	+	Silent	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		RNA-Seq	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:29797394G>A	ENST00000360323.6	+	4	843	c.819G>A	c.(817-819)gtG>gtA	p.V273V	HLA-G_ENST00000376818.3_Silent_p.V181V|HLA-G_ENST00000376828.2_Silent_p.V278V|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.V273V			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	273	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CTGTGGTGGTGCCTTCTGGAG	0.627																																					p.V273V													.	HLA-G	90		0			c.G819A												63.0	58.0	60.0					6																	29797394		2203	4296	6499	SO:0001819	synonymous_variant	3135	exon5			GGTGGTGCCTTCT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.819G>A	6.37:g.29797394G>A			137	0	0		132	0.01	1	NM_002127	866	0.40	344		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																					0.627	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076286.2		NM_002127	
TRIM39	56658	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	30309904	30309904	+	Silent	SNP	A	A	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:30309904A>G	ENST00000396547.1	+	8	1585	c.1425A>G	c.(1423-1425)acA>acG	p.T475T	TRIM39_ENST00000540416.1_Silent_p.T445T|TRIM39-RPP21_ENST00000513556.1_Intron|TRIM39_ENST00000396551.3_Silent_p.T445T|TRIM39_ENST00000376659.5_Silent_p.T445T|TRIM39_ENST00000396548.1_Silent_p.T445T|TRIM39_ENST00000376656.4_Silent_p.T475T			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	475	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						ACAATGTCACAGACCGCTCTC	0.507																																					p.T475T													.	.			0			c.A1425G												93.0	88.0	90.0					6																	30309904		1511	2708	4219	SO:0001819	synonymous_variant	56658	exon9			TGTCACAGACCGC	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.1425A>G	6.37:g.30309904A>G			130	0	0		86	0.08	7	NM_021253	42	0.00	0	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1																																																																																					0.507	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000076086.2		NM_172016	
RPL3P2	116935	bcgsc.ca	37	6	31248785	31248785	+	IGR	SNP	G	G	A	rs2524061	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:31248785G>A								HLA-C (8922 upstream) : XXbac-BPG248L24.13 (12899 downstream)																							GTCACCAGTCGTTGGCACACC	0.567													g|||	499	0.0996406	0.093	0.1455	5008	,	,		21524	0.1022		0.1143	False		,,,				2504	0.0583				.													.	.			0			.																																									SO:0001628	intergenic_variant	116935	.			CCAGTCGTTGGCA																													6.37:g.31248785G>A			48	0	0		57	0.09	5	.	9	0.00	0		RNA	SNP		37																																																																																					0	0.567										
HLA-DRB9	3132	bcgsc.ca	37	6	32441276	32441276	+	IGR	SNP	C	C	T	rs12215313	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:32441276C>T								HLA-DRA (28453 upstream) : HLA-DRB5 (43843 downstream)																							GCGGGAGCCTCCAGGGAGCTT	0.572													C|||	1451	0.289736	0.1853	0.4092	5008	,	,		16525	0.3095		0.3211	False		,,,				2504	0.2935				.													.	.			0			.																																									SO:0001628	intergenic_variant	3132	.			GAGCCTCCAGGGA																													6.37:g.32441276C>T			129	0	0		129	0.05	6	.	277	0.00	0		RNA	SNP		37																																																																																					0	0.572										
HLA-DRB6	3128	broad.mit.edu	37	6	32521925	32521926	+	RNA	INS	-	-	T	rs536244238|rs112961196		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:32521925_32521926insT	ENST00000411500.1	-	0	740					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		AAATCACACTGAACAGTTACAA	0.366																																					.													.	.			0			.																																											0	.			CACACTGAACAGT	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32521925_32521926insT			14	0	0		10	0.30	3	.	0		0		RNA	INS	ENST00000411500.1	37																																																																																						0.366	HLA-DRB6-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000272900.1		NR_001298	
Unknown	0	bcgsc.ca	37	6	51275042	51275042	+	IGR	SNP	T	T	C	rs62458490	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:51275042T>C								TFAP2B (459716 upstream) : SNORD66 (54445 downstream)														p.K21R(1)									CTGGACTTGCTTGAGGTACTG	0.463													T|||	1682	0.335863	0.3956	0.5072	5008	,	,		19769	0.255		0.2614	False		,,,				2504	0.2935				.													ENSG00000180518,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	stomach(1)	.																																									SO:0001628	intergenic_variant	0	.			ACTTGCTTGAGGT																													6.37:g.51275042T>C			436	0.002293578	1		355	0.03	12	.	162	0.00	0		RNA	SNP		37																																																																																					0	0.463										
CLNS1AP1	1204	bcgsc.ca	37	6	54350048	54350048	+	IGR	SNP	G	G	A	rs807991	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:54350048G>A								TINAG (95098 upstream) : RNU6-1023P (301136 downstream)																							ATCTTATTGAGTCTTCTGTCC	0.423													A|||	2509	0.500998	0.447	0.5533	5008	,	,		19572	0.6478		0.3976	False		,,,				2504	0.4918				.													.	.			0			.																																									SO:0001628	intergenic_variant	1204	.			TATTGAGTCTTCT																													6.37:g.54350048G>A			124	0	0		115	0.05	6	.	0		0		RNA	SNP		37																																																																																					0	0.423										
ADH5P4	642443	bcgsc.ca	37	6	66546941	66546941	+	IGR	SNP	A	A	G	rs61732140	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:66546941A>G								EYS (129823 upstream) : AC002485.1 (522376 downstream)																							TTTTTTGGACATATATTCAGA	0.403													A|||	32	0.00638978	0.0008	0.0072	5008	,	,		19369	0.0		0.0179	False		,,,				2504	0.0082				.													.	.			0			.																																									SO:0001628	intergenic_variant	642443	.			TTGGACATATATT																													6.37:g.66546941A>G			313	0.0031948882	1		269	0.04	12	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.403										
ADH5P4	642443	bcgsc.ca	37	6	66547178	66547178	+	IGR	SNP	G	G	A	rs4392709	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:66547178G>A								EYS (130060 upstream) : AC002485.1 (522139 downstream)																							TCCATCAGTCGTCTCAATGAG	0.453													A|||	3607	0.720248	0.6339	0.7435	5008	,	,		20579	0.8611		0.6004	False		,,,				2504	0.7986				.													.	.			0			.																																									SO:0001628	intergenic_variant	642443	.			TCAGTCGTCTCAA																													6.37:g.66547178G>A			237	0.0042194093	1		154	0.09	14	.	0		0		RNA	SNP		37																																																																																					0	0.453										
ADH5P4	642443	bcgsc.ca	37	6	66547322	66547322	+	IGR	SNP	T	T	G	rs9363455	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:66547322T>G								EYS (130204 upstream) : AC002485.1 (521995 downstream)																							TTTACAGCCCTTGATAACTGC	0.483													t|||	3205	0.639976	0.4266	0.6931	5008	,	,		19445	0.7937		0.5905	False		,,,				2504	0.7832				.													.	.			0			.																																									SO:0001628	intergenic_variant	642443	.			CAGCCCTTGATAA																													6.37:g.66547322T>G			156	0	0		107	0.11	12	.	0		0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	6	73308220	73308220	+	IGR	SNP	G	G	C	rs79957120	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:73308220G>C								RIMS1 (195375 upstream) : KCNQ5 (23299 downstream)																							CTCCTTTTTGGTACTGACTCT	0.348													G|||	3	0.000599042	0.0	0.0	5008	,	,		18110	0.0		0.003	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTTGGTACTGA																													6.37:g.73308220G>C			148	0	0		106	0.05	5	.	0		0		RNA	SNP		37																																																																																					0	0.348										
PHIP	55023	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	79725372	79725372	+	Missense_Mutation	SNP	G	G	C			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:79725372G>C	ENST00000275034.4	-	14	1531	c.1364C>G	c.(1363-1365)aCt>aGt	p.T455S		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	455					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TAGTTGACCAGTGTAAGAATT	0.323																																					p.T455S													.	.			0			c.C1364G												142.0	134.0	137.0					6																	79725372		2203	4299	6502	SO:0001583	missense	55023	exon14			TGACCAGTGTAAG	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.1364C>G	6.37:g.79725372G>C	ENSP00000275034:p.Thr455Ser		130	0	0		118	0.08	10	NM_017934	7	0.00	0	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939891	0.52972	.	.	ENSG00000146247	ENST00000275034	T	0.19532	2.14	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.069902	0.64402	D	0.000014	T	0.30885	0.0779	L	0.46614	1.455	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.70716	0.97;0.97	T	0.00722	-1.1594	9	.	.	.	-9.9846	18.3005	0.90162	0.0:0.0:1.0:0.0	.	455;455	A7J992;Q8WWQ0	.;PHIP_HUMAN	S	455	ENSP00000275034:T455S	.	T	-	2	0	PHIP	79782091	1.000000	0.71417	0.967000	0.41034	0.968000	0.65278	6.108000	0.71522	2.647000	0.89833	0.591000	0.81541	ACT			0.323	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041297.2			
Unknown	0	bcgsc.ca	37	6	85996401	85996401	+	IGR	SNP	C	C	T	rs313229	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:85996401C>T								TBX18 (522164 upstream) : RP11-30P6.6 (100535 downstream)																							TGTGAGCAAGCAGTGTGGGCA	0.463													C|||	2728	0.544728	0.6097	0.4986	5008	,	,		16247	0.6498		0.3728	False		,,,				2504	0.5583				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGCAAGCAGTGTG																													6.37:g.85996401C>T			278	0.0035971223	1		252	0.06	15	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.463										
RNU4-70P	106480548	bcgsc.ca	37	6	97096688	97096688	+	RNA	SNP	T	T	C	rs11759390	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:97096688T>C	ENST00000384579.1	-	0	139									RNA, U4 small nuclear 70, pseudogene																		TGCTTCCCACTGAACTTTTTC	0.423													T|||	172	0.034345	0.0257	0.0562	5008	,	,		20467	0.0		0.0577	False		,,,				2504	0.0419				.													.	.			0			.																																											442237	.			TCCCACTGAACTT			6q16.1	2013-04-03			ENSG00000207309	ENSG00000207309			47006	pseudogene	RNA, pseudogene							Standard			Approved						6.37:g.97096688T>C			182	0	0		132	0.11	15	.	0		0		RNA	SNP	ENST00000384579.1	37																																																																																						0.423	RNU4-70P-201	KNOWN	basic	snRNA	snRNA					
MED23	9439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	131923359	131923359	+	Splice_Site	SNP	T	T	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:131923359T>G	ENST00000368068.3	-	17	2273	c.2094A>C	c.(2092-2094)acA>acC	p.T698T	MED23_ENST00000368053.4_Splice_Site_p.T704T|MED23_ENST00000368058.1_Splice_Site_p.T704T|MED23_ENST00000403834.3_Splice_Site_p.T704T|MED23_ENST00000545957.1_Splice_Site_p.T339T|MED23_ENST00000368060.3_Splice_Site_p.T698T|MED23_ENST00000540546.1_Splice_Site_p.T704T|MED23_ENST00000354577.4_Splice_Site_p.T704T	NM_004830.3	NP_004821.2	Q9ULK4	MED23_HUMAN	mediator complex subunit 23	698					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	44	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)		TCACCGTACCTGTTACATGAG	0.378																																					p.T704T													.	.			0			c.A2112C												144.0	128.0	133.0					6																	131923359		2203	4300	6503	SO:0001630	splice_region_variant	9439	exon18			CGTACCTGTTACA	AF104255	CCDS5146.1, CCDS5147.1, CCDS59039.1	6q22.33-q24.1	2008-02-05	2007-08-08	2007-07-30	ENSG00000112282	ENSG00000112282			2372	protein-coding gene	gene with protein product		605042	"""cofactor required for Sp1 transcriptional activation, subunit 3, 130kDa"""	CRSP3		9989412	Standard	NM_004830		Approved	CRSP130, DRIP130, Sur2	uc003qcs.2	Q9ULK4	OTTHUMG00000015565	ENST00000368068.3:c.2095+1A>C	6.37:g.131923359T>G			130	0	0		100	0.26	26	NM_015979	23	0.43	10	B9TX55|O95403|Q5JWT3|Q5JWT4|Q6P9H6|Q9H0J2|Q9NTT9|Q9NTU0|Q9Y5P7|Q9Y667	Silent	SNP	ENST00000368068.3	37	CCDS5147.1																																																																																					0.378	MED23-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000042215.1			Silent
BTF3L4P3	391040	bcgsc.ca	37	6	137865140	137865140	+	IGR	SNP	A	A	G	rs9484059	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:137865140A>G								SNORD112 (3532 upstream) : RP11-95M15.1 (129456 downstream)																							ACTGTCCAAGACTTGCCATGG	0.418													A|||	1272	0.253994	0.3185	0.1787	5008	,	,		19014	0.3631		0.1491	False		,,,				2504	0.2157				.													.	.			0			.																																									SO:0001628	intergenic_variant	391040	.			TCCAAGACTTGCC																													6.37:g.137865140A>G			120	0	0		74	0.08	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.418										
BTF3L4P3	391040	bcgsc.ca	37	6	137865147	137865147	+	IGR	SNP	A	A	G	rs9494809	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:137865147A>G								SNORD112 (3539 upstream) : RP11-95M15.1 (129449 downstream)																							AAGACTTGCCATGGGAACTGT	0.418													A|||	1342	0.267971	0.3691	0.183	5008	,	,		18970	0.3631		0.1491	False		,,,				2504	0.2157				.													.	.			0			.																																									SO:0001628	intergenic_variant	391040	.			CTTGCCATGGGAA																													6.37:g.137865147A>G			126	0	0		71	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.418										
SRP72P2	153932	bcgsc.ca	37	6	158658759	158658759	+	IGR	SNP	C	C	G	rs113731832	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:158658759C>G								GTF2H5 (38383 upstream) : RP11-732M18.3 (44535 downstream)																							TTGACTATCTCTAGTAACTTT	0.378													c|||	89	0.0177716	0.0151	0.0331	5008	,	,		20357	0.0		0.0408	False		,,,				2504	0.0051				.													.	.			0			.																																									SO:0001628	intergenic_variant	153932	.			CTATCTCTAGTAA																													6.37:g.158658759C>G			57	0	0		37	0.11	4	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.378										
SRP72P2	153932	bcgsc.ca	37	6	158658857	158658857	+	IGR	SNP	A	A	C	rs112542076	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:158658857A>C								GTF2H5 (38481 upstream) : RP11-732M18.3 (44437 downstream)																							ATGATGGCAAATGTTTACTAA	0.388													a|||	89	0.0177716	0.0151	0.0331	5008	,	,		19315	0.0		0.0408	False		,,,				2504	0.0051				.													.	.			0			.																																									SO:0001628	intergenic_variant	153932	.			TGGCAAATGTTTA																													6.37:g.158658857A>C			51	0	0		50	0.14	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.388										
TCP1	6950	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	160205000	160205000	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:160205000G>A	ENST00000321394.7	-	7	1050	c.770C>T	c.(769-771)cCt>cTt	p.P257L	TCP1_ENST00000392168.2_Missense_Mutation_p.P102L|TCP1_ENST00000544255.1_Missense_Mutation_p.P33L|SNORA29_ENST00000384183.1_RNA|TCP1_ENST00000420894.2_Missense_Mutation_p.P257L	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	257					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		CAGTTTTTCAGGGTCTGTAAT	0.398																																					p.P257L													.	.			0			c.C770T												131.0	120.0	124.0					6																	160205000		2203	4300	6503	SO:0001583	missense	6950	exon7			TTTTCAGGGTCTG	X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"""Heat Shock Proteins / Chaperonins"""	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.770C>T	6.37:g.160205000G>A	ENSP00000317334:p.Pro257Leu		168	0	0		127	0.16	20	NM_030752	618	0.17	105	E1P5B2|Q15556|Q5TCM3	Missense_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898543	0.91962	.	.	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000420894;ENST00000392168;ENST00000539756	T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.88429	0.6434	M	0.91354	3.2	0.80722	D	1	B;P	0.41008	0.403;0.735	B;P	0.55222	0.367;0.771	D	0.89596	0.3831	10	0.72032	D	0.01	-28.2934	19.5771	0.95449	0.0:0.0:1.0:0.0	.	257;257	E7ERF2;P17987	.;TCPA_HUMAN	L	257;33;257;102;55	ENSP00000317334:P257L;ENSP00000439447:P33L;ENSP00000390159:P257L;ENSP00000376008:P102L;ENSP00000441345:P55L	ENSP00000317334:P257L	P	-	2	0	TCP1	160124990	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.273000	0.95719	2.617000	0.88574	0.555000	0.69702	CCT			0.398	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000042917.2		NM_030752	
Unknown	0	bcgsc.ca	37	6	167622347	167622347	+	IGR	SNP	A	A	C	rs9459922	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:167622347A>C								TCP10L2 (11954 upstream) : RP11-568A7.3 (28648 downstream)																							TGGCGAAGGCAGCTTCCTTGC	0.577													A|||	1210	0.241613	0.115	0.1916	5008	,	,		18993	0.3532		0.2286	False		,,,				2504	0.3466				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAAGGCAGCTTCC																													6.37:g.167622347A>C			113	0	0		85	0.09	8	.	13	0.00	0		RNA	SNP		37																																																																																					0	0.577										
CTAGE13P	100421638	bcgsc.ca	37	6	168688281	168688281	+	IGR	SNP	T	T	G	rs9456019	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr6:168688281T>G								RP11-503C24.4 (25020 upstream) : DACT2 (5228 downstream)																							TTCTCCTCTTTCCTTGGTAAT	0.552													T|||	1267	0.252995	0.0272	0.3516	5008	,	,		18559	0.2083		0.4632	False		,,,				2504	0.318				.													.	.			0			.																																									SO:0001628	intergenic_variant	100421638	.			CCTCTTTCCTTGG																													6.37:g.168688281T>G			159	0.0062893082	1		127	0.13	17	.	0		0		RNA	SNP		37																																																																																					0	0.552										
RBAK-RBAKDN	100533952	bcgsc.ca	37	7	5112853	5112853	+	IGR	SNP	G	G	C	rs73316654	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:5112853G>C	ENST00000396904.2	+	0	766				RBAKDN_ENST00000498308.1_lincRNA	NM_001204513.1	NP_001191442.1			RBAK-RBAKDN readthrough																		TTCTTAGCTAGAGGTGCTGTT	0.577													G|||	135	0.0269569	0.0991	0.0058	5008	,	,		18757	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.							G		368,4038		8,352,1843	38.0	38.0	38.0			-2.1	0.0	7	dbSNP_130	38	7,8585		0,7,4289	yes	utr-3	RBAK-LOC389458	NM_001204513.1		8,359,6132	CC,CG,GG		0.0815,8.3522,2.8851			5112853	375,12623	2203	4296	6499	SO:0001628	intergenic_variant	57786	.			TAGCTAGAGGTGC		CCDS56463.1	7p22.1	2013-05-20				ENSG00000272968			42971	other	readthrough							Standard	NM_001204513		Approved				OTTHUMG00000186010		7.37:g.5112853G>C			168	0	0		143	0.04	6	.	0		0		RNA	SNP	ENST00000396904.2	37	CCDS56463.1																																																																																					0.577	RBAK-RBAKDN-002	KNOWN	basic|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000472011.1			
Unknown	0	bcgsc.ca	37	7	9767725	9767725	+	IGR	SNP	G	G	T	rs72583761	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:9767725G>T								AC079756.1 (133372 upstream) : AC060834.3 (9225 downstream)																							TCTGGGTTCCGGCTGACTCCT	0.572													g|||	965	0.192692	0.1747	0.2522	5008	,	,		17427	0.3948		0.0467	False		,,,				2504	0.1166				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGTTCCGGCTGAC																													7.37:g.9767725G>T			175	0	0		157	0.08	12	.	13	0.00	0		RNA	SNP		37																																																																																					0	0.572										
Unknown	0	bcgsc.ca	37	7	9767811	9767811	+	IGR	SNP	T	T	G	rs112406696	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:9767811T>G								AC079756.1 (133458 upstream) : AC060834.3 (9139 downstream)																							TGGTCCTTTTTGGTGGGCTGG	0.572													t|||	1152	0.230032	0.3003	0.2695	5008	,	,		16146	0.3978		0.0527	False		,,,				2504	0.1166				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTTTTTGGTGGG																													7.37:g.9767811T>G			162	0	0		156	0.09	14	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.572										
Unknown	0	bcgsc.ca	37	7	12511173	12511173	+	IGR	SNP	C	C	T	rs12699379	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:12511173C>T								VWDE (67642 upstream) : AC005281.1 (24881 downstream)																							CAGACTTTAACGTAATTGTGG	0.368													C|||	1644	0.328275	0.1589	0.4669	5008	,	,		18314	0.4752		0.2217	False		,,,				2504	0.4172				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTTAACGTAATT																													7.37:g.12511173C>T			46	0	0		27	0.15	4	.	0		0		RNA	SNP		37																																																																																					0	0.368										
Unknown	0	bcgsc.ca	37	7	12511312	12511312	+	IGR	SNP	G	G	A	rs11275	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:12511312G>A								VWDE (67781 upstream) : AC005281.1 (24742 downstream)																							AAACAGATCTGTTTATATTAA	0.333													G|||	1269	0.253395	0.4115	0.17	5008	,	,		17805	0.2163		0.2127	False		,,,				2504	0.1789				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGATCTGTTTATA																													7.37:g.12511312G>A			87	0	0		71	0.07	5	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	7	12511924	12511924	+	IGR	SNP	T	T	G	rs847956	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:12511924T>G								VWDE (68393 upstream) : AC005281.1 (24130 downstream)																							AAGAAGCACTTAAAAAAATAA	0.383													G|||	1270	0.253594	0.4115	0.17	5008	,	,		18454	0.2163		0.2137	False		,,,				2504	0.1789				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGCACTTAAAAAA																													7.37:g.12511924T>G			58	0	0		51	0.14	7	.	0		0		RNA	SNP		37																																																																																					0	0.383										
Unknown	0	bcgsc.ca	37	7	23603318	23603318	+	IGR	SNP	A	A	G	rs227944	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:23603318A>G								TRA2A (31658 upstream) : CCDC126 (33679 downstream)																							TTCAGTCCAAAATAGATCCCA	0.393													A|||	972	0.194089	0.0045	0.1902	5008	,	,		20432	0.4246		0.1809	False		,,,				2504	0.229				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTCCAAAATAGAT																													7.37:g.23603318A>G			369	0	0		325	0.04	13	.	0		0		RNA	SNP		37																																																																																					0	0.393										
ZNRF2P2	100271874	bcgsc.ca	37	7	29700039	29700039	+	RNA	SNP	C	C	T	rs1728603	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:29700039C>T	ENST00000426767.1	-	0	366					NR_024278.1				zinc and ring finger 2 pseudogene 2																		TACAGTAAAACGCTTCCATCT	0.313													t|||	1321	0.263778	0.3487	0.3501	5008	,	,		14511	0.0595		0.3618	False		,,,				2504	0.1973				.													.	.			0			.																																											0	.			GTAAAACGCTTCC			7p14.3	2011-08-22			ENSG00000239968	ENSG00000225264			42793	pseudogene	pseudogene							Standard	NR_027347		Approved				OTTHUMG00000152750		7.37:g.29700039C>T			174	0	0		156	0.13	20	.	0		0		RNA	SNP	ENST00000426767.1	37																																																																																						0.313	ZNRF2P2-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000327679.1		NR_027347	
TRGC2	6967	broad.mit.edu	37	7	38284884	38284885	+	RNA	INS	-	-	GG	rs138091320|rs200076851|rs377514954		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:38284884_38284885insGG	ENST00000436911.2	-	0	330							P03986	TRGC2_HUMAN	T cell receptor gamma constant 2						immune response (GO:0006955)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)										TTATTTGTCAAGgtgtgtgtgt	0.391																																					.													.	.			0			.																																											0	.			TTGTCAAGGTGTG	M15002		7p14	2012-02-07			ENSG00000227191	ENSG00000227191		"""T cell receptors / TRG locus"""	12276	other	T cell receptor gene	"""T-cell receptor, gamma, constant region C2"""	615450		TCRGC2		3458221	Standard	NG_001336		Approved	TRGC2(2X), TRGC2(3X)		P03986	OTTHUMG00000155215		7.37:g.38284885_38284886dupGG			4	0	0		7	0.71	5	.	0		0		RNA	INS	ENST00000436911.2	37																																																																																						0.391	TRGC2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene		OTTHUMT00000338821.2		NG_001336	
Unknown	0	bcgsc.ca	37	7	39874281	39874281	+	IGR	SNP	T	T	C	rs113205984	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:39874281T>C								LINC00265 (41590 upstream) : RN7SL496P (53690 downstream)																							CCTTTCAGAATGACAATTATT	0.517													N|||	1742	0.347843	0.4342	0.304	5008	,	,		18870	0.2907		0.3161	False		,,,				2504	0.3538				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCAGAATGACAAT																													7.37:g.39874281T>C			204	0	0		163	0.09	14	.	35	1.00	35		RNA	SNP		37																																																																																					0	0.517										
AC004899.1	0	bcgsc.ca	37	7	48886607	48886607	+	5'Flank	SNP	A	A	G	rs28657654	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:48886607A>G	ENST00000596947.1	+	0	0																											AGAAAAGATCATGGTGATCGA	0.388													A|||	933	0.186302	0.0076	0.1916	5008	,	,		19130	0.2946		0.2028	False		,,,				2504	0.2955				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			AAGATCATGGTGA																													7.37:g.48886607A>G	Exception_encountered		230	0.0043478261	1		194	0.09	17	.	2	0.00	0		RNA	SNP	ENST00000596947.1	37																																																																																						0.388	AC004899.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
GDI2P1	2667	bcgsc.ca	37	7	48943352	48943352	+	IGR	SNP	T	T	C	rs887451	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:48943352T>C								AC004899.1 (52131 upstream) : AC010971.1 (326380 downstream)																							AGTAGTGTTATAGAGGCACTC	0.408													T|||	2730	0.545128	0.4312	0.5461	5008	,	,		19115	0.6558		0.5905	False		,,,				2504	0.5378				.													.	.			0			.																																									SO:0001628	intergenic_variant	2667	.			GTGTTATAGAGGC																													7.37:g.48943352T>C			25	0	0		23	0.22	5	.	0		0		RNA	SNP		37																																																																																					0	0.408										
ROBO2P1	106480790	bcgsc.ca	37	7	51668140	51668140	+	IGR	SNP	G	G	A	rs4538818	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:51668140G>A								COBL (283625 upstream) : RP4-718N17.2 (13806 downstream)																							TCATGAATTCGAACTTTGTCT	0.473													G|||	1013	0.202276	0.1036	0.1844	5008	,	,		16463	0.2569		0.2714	False		,,,				2504	0.2209				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAATTCGAACTTT																													7.37:g.51668140G>A			158	0	0		132	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.473										
ROBO2P1	106480790	bcgsc.ca	37	7	51668190	51668190	+	IGR	SNP	G	G	A	rs4541850	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:51668190G>A								COBL (283675 upstream) : RP4-718N17.2 (13756 downstream)																							TCCCTGGGGAGGCTGGCACTC	0.473													G|||	1013	0.202276	0.1036	0.1844	5008	,	,		15859	0.2569		0.2714	False		,,,				2504	0.2209				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGGGAGGCTGGC																													7.37:g.51668190G>A			185	0	0		159	0.04	7	.	0		0		RNA	SNP		37																																																																																					0	0.473										
HAUS6P1	653175	bcgsc.ca	37	7	53256324	53256324	+	IGR	SNP	T	T	C	rs35856447	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:53256324T>C								POM121L12 (151707 upstream) : RNU1-14P (177426 downstream)																							GACACAAAGATGGGAACTCCC	0.378													T|||	1102	0.220048	0.0598	0.2017	5008	,	,		18767	0.1935		0.331	False		,,,				2504	0.363				.													.	.			0			.																																									SO:0001628	intergenic_variant	653175	.			CAAAGATGGGAAC																													7.37:g.53256324T>C			238	0.0084033613	2		215	0.10	22	.	11	0.00	0		RNA	SNP		37																																																																																					0	0.378										
SLC25A5P3	222005	bcgsc.ca	37	7	54487594	54487594	+	IGR	SNP	C	C	T	rs35588876	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:54487594C>T								snoU13 (59906 upstream) : VSTM2A (122423 downstream)																							AAGGGAATTCCGAGGCCTCTG	0.493													C|||	1507	0.300919	0.0908	0.3285	5008	,	,		20483	0.4087		0.3419	False		,,,				2504	0.4121				.													.	.			0			.																																									SO:0001628	intergenic_variant	222005	.			GAATTCCGAGGCC																													7.37:g.54487594C>T			48	0	0		35	0.11	4	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.493										
CDC42P2	643336	bcgsc.ca	37	7	55706496	55706496	+	IGR	SNP	T	T	C	rs7791528	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:55706496T>C								RP11-310H4.3 (43797 upstream) : FKBP9L (42270 downstream)																							GTTTTACCAATAGCACCATCG	0.378													t|||	1153	0.230232	0.2277	0.1542	5008	,	,		20238	0.2232		0.2654	False		,,,				2504	0.2587				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TACCAATAGCACC																													7.37:g.55706496T>C			42	0	0		39	0.21	8	.	0		0		RNA	SNP		37																																																																																					0	0.378										
FKBP9P1	360132	bcgsc.ca	37	7	55774888	55774888	+	IGR	SNP	C	C	T	rs12666519	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:55774888C>T								FKBP9L (17894 upstream) : RNU6-1126P (82172 downstream)																							CATCCAGAAGCGTGCCATTGT	0.438													C|||	1471	0.29373	0.3865	0.196	5008	,	,		18248	0.4196		0.1034	False		,,,				2504	0.3037				.													.	.			0			.																																									SO:0001628	intergenic_variant	360132	.			CAGAAGCGTGCCA																													7.37:g.55774888C>T			335	0	0		328	0.08	25	.	13	0.00	0		RNA	SNP		37																																																																																					0	0.438										
Unknown	0	bcgsc.ca	37	7	56356744	56356744	+	IGR	SNP	G	G	T	rs3813510	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:56356744G>T								AC073136.1 (19200 upstream) : RNU6-1335P (51179 downstream)																							ATTACAGTCTGCTGGGTCTTT	0.398													G|||	2106	0.420527	0.1241	0.4827	5008	,	,		19573	0.4702		0.5815	False		,,,				2504	0.5603				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGTCTGCTGGGT																													7.37:g.56356744G>T			81	0.012345679	1		56	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.398										
GUSBP6	653435	bcgsc.ca	37	7	63602199	63602199	+	RNA	SNP	A	A	G	rs191758847	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:63602199A>G	ENST00000434932.1	+	0	115				RP11-321E8.4_ENST00000442436.1_lincRNA					glucuronidase, beta pseudogene 6																		TGAGGTGGCAATGACAAATTT	0.463													A|||	2	0.000399361	0.0015	0.0	5008	,	,		18858	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																											0	.			GTGGCAATGACAA			7q11.21	2011-06-09			ENSG00000224458	ENSG00000224458			42320	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000156481		7.37:g.63602199A>G			31	0	0		31	0.13	4	.	2	0.00	0		RNA	SNP	ENST00000434932.1	37																																																																																						0.463	GUSBP6-002	KNOWN	basic|exp_conf	processed_transcript	pseudogene		OTTHUMT00000344314.1			
CCT6P3	643180	broad.mit.edu	37	7	64528813	64528814	+	RNA	INS	-	-	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:64528813_64528814insT	ENST00000426828.1	+	0	621				SNORA15_ENST00000384334.1_RNA|SNORA22_ENST00000384614.1_RNA	NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3																		CTTTCTGTAACTTTTTTTTTTT	0.317																																					.													.	.			0			.																																											0	.			CTGTAACTTTTTT			7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585			35137	pseudogene	pseudogene							Standard	NR_033416		Approved		uc010kzt.1		OTTHUMG00000156630		7.37:g.64528824_64528824dupT			7	0	0		9	0.22	2	.	0		0		RNA	INS	ENST00000426828.1	37																																																																																						0.317	CCT6P3-004	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000344862.1			
GTF2IP5	100420546	bcgsc.ca	37	7	65266945	65266945	+	IGR	SNP	G	G	A	rs73701013	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:65266945G>A								CCT6P1 (38604 upstream) : RNU6-912P (12713 downstream)																							CCGAGTTCCTGTATGTAGAAG	0.423																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCCTGTATGTA																													7.37:g.65266945G>A			39	0	0		45	0.11	5	.	0		0		RNA	SNP		37																																																																																					0	0.423										
AUTS2	26053	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	70255922	70255922	+	Silent	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:70255922G>T	ENST00000342771.4	+	19	4041	c.3720G>T	c.(3718-3720)ctG>ctT	p.L1240L	AUTS2_ENST00000406775.2_Silent_p.L1216L	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1240										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CGACTCCTCTGTCCGCAGAGA	0.622																																					p.L1240L													.	.			0			c.G3720T												26.0	28.0	27.0					7																	70255922		2201	4299	6500	SO:0001819	synonymous_variant	26053	exon19			TCCTCTGTCCGCA	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3720G>T	7.37:g.70255922G>T			83	0	0		69	0.16	11	NM_015570	121	0.25	30	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1																																																																																					0.622	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000251971.2			
POMZP3	22932	bcgsc.ca	37	7	76247668	76247668	+	Intron	SNP	G	G	A	rs1636619		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:76247668G>A	ENST00000310842.4	-	4	912				UPK3B_ENST00000443097.2_Intron|UPK3B_ENST00000419923.2_Intron|AC004980.7_ENST00000418663.1_RNA|POMZP3_ENST00000275569.4_Intron	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion											kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				gccgggcaccgtggctcacgc	0.542																																					.													.	.			0			.							G	,	632,3772		25,582,1595	91.0	82.0	85.0		,			7	dbSNP_89	85	1379,7215		5,1369,2923	no	intron,intron	POMZP3	NM_012230.3,NM_152992.2	,	30,1951,4518	AA,AG,GG		16.0461,14.3506,15.4716	,	,	76247668	2011,10987	2202	4297	6499	SO:0001627	intron_variant	22932	.			GGCACCGTGGCTC	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"""POM-ZP3 fusion protein"", ""POM121/ZP3 fusion protein"""	600587	"""POM (POM121 rat homolog) and ZP3 fusion"", ""POM (POM121 homolog, rat) and ZP3 fusion"""			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.228-51C>T	7.37:g.76247668G>A			529	0.0075614367	4		489	0.09	43	.	1	0.00	0	F6STJ3|Q12903|Q9BWB4	Silent	SNP	ENST00000310842.4	37	CCDS43606.1																																																																																					0.542	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000341775.1		NM_012230	
Unknown	0	bcgsc.ca	37	7	79726151	79726151	+	IGR	SNP	G	G	T	rs10239304	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:79726151G>T								RNU6-849P (184627 upstream) : GNAI1 (37662 downstream)																							GGATAAACATGATGACTTGAC	0.522													G|||	1518	0.303115	0.2617	0.3141	5008	,	,		19150	0.3095		0.333	False		,,,				2504	0.3139				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAACATGATGACT																													7.37:g.79726151G>T			28	0	0		33	0.30	10	.	0		0		RNA	SNP		37																																																																																					0	0.522										
ZNF804B	219578	bcgsc.ca	37	7	88964226	88964227	+	Missense_Mutation	DNP	CC	CC	AG	rs71526642|rs76870774|rs79931924	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:88964226_88964227CC>AG	ENST00000333190.4	+	4	2539_2540	c.1930_1931CC>AG	c.(1930-1932)CCt>AGt	p.P644S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	644							metal ion binding (GO:0046872)	p.P644R(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TCCCTGCAGTCCTCATTTGGAA	0.406										HNSCC(36;0.09)																											p.P644S													ZNF804B,NS,carcinoma,0,1	ZNF804B	322	1	1	Substitution - Missense(1)	pancreas(1)	c.C1931G																																									SO:0001583	missense	219578	exon4			TGCAGTCCTCATT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	Exception_encountered	7.37:g.88964226_88964227delinsAG	ENSP00000329638:p.Pro644Ser		194	0	0		162	0.04	7	NM_181646	0		0	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	DNP	ENST00000333190.4	37	CCDS5613.1																																																																																					0.406	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253683.2		NM_181646	
KEL	3792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	142651427	142651427	+	Missense_Mutation	SNP	C	C	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:142651427C>G	ENST00000355265.2	-	8	1242	c.768G>C	c.(766-768)caG>caC	p.Q256H	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	256					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					AGGTTCCCAGCTGATTCAGGT	0.542																																					p.Q256H													.	.			0			c.G768C												108.0	109.0	109.0					7																	142651427		2203	4300	6503	SO:0001583	missense	3792	exon8			TCCCAGCTGATTC	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.768G>C	7.37:g.142651427C>G	ENSP00000347409:p.Gln256His		103	0	0		73	0.30	22	NM_000420	91	0.26	24	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223393	0.39300	.	.	ENSG00000197993	ENST00000355265	D	0.82803	-1.65	6.07	-7.81	0.01210	Peptidase M13 (1);	0.922401	0.09036	N	0.857925	D	0.82724	0.5099	M	0.68952	2.095	0.19300	N	0.999977	D	0.54397	0.966	P	0.60345	0.873	T	0.73764	-0.3880	10	0.66056	D	0.02	-9.3576	2.0959	0.03667	0.1849:0.136:0.3934:0.2857	.	256	P23276	KELL_HUMAN	H	256	ENSP00000347409:Q256H	ENSP00000347409:Q256H	Q	-	3	2	KEL	142361549	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-1.940000	0.01543	-1.093000	0.03058	-0.982000	0.02568	CAG			0.542	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000347671.2		NM_000420	
AC099552.4	0	bcgsc.ca;mdanderson.org	37	7	154989982	154989982	+	Missense_Mutation	SNP	G	G	A	rs28664023	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:154989982G>A	ENST00000404289.1	-	1	164	c.29C>T	c.(28-30)tCg>tTg	p.S10L																								GGCTCACCCCGAATCACTCAG	0.522													G|||	1484	0.296326	0.2209	0.281	5008	,	,		20551	0.3452		0.2744	False		,,,				2504	0.3814				.													.	.			0			.																																									SO:0001583	missense	0	.			CACCCCGAATCAC																												ENST00000404289.1:c.29C>T	7.37:g.154989982G>A	ENSP00000386035:p.Ser10Leu		204	0	0		180	0.14	26	.	0		0		Missense_Mutation	SNP	ENST00000404289.1	37		621	0.28434065934065933	125	0.2540650406504065	99	0.27348066298342544	193	0.3374125874125874	204	0.2691292875989446	G	3.348	-0.133170	0.06711	.	.	ENSG00000217825	ENST00000404289	.	.	.	1.4	-1.65	0.08291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33240	-0.9876	4	0.87932	D	0	.	5.9314	0.19140	0.0:0.0:0.5699:0.4301	rs28664023	.	.	.	L	10	.	ENSP00000386035:S10L	S	-	2	0	AC099552.4	154620915	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.277000	0.08502	-0.455000	0.07054	-0.520000	0.04383	TCG			0.522	AC099552.4-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000322236.1			
AC008060.7	0	bcgsc.ca	37	7	155174898	155174898	+	Missense_Mutation	SNP	C	C	G			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr7:155174898C>G	ENST00000401499.1	+	1	128	c.80C>G	c.(79-81)gCc>gGc	p.A27G																								CGGCGGGGAGCCTGGCTGAAG	0.642																																					.													.	.			0			.																																									SO:0001583	missense	0	.			GGGGAGCCTGGCT																												ENST00000401499.1:c.80C>G	7.37:g.155174898C>G	ENSP00000384676:p.Ala27Gly		39	0	0		66	0.09	6	.	0		0		Missense_Mutation	SNP	ENST00000401499.1	37		.	.	.	.	.	.	.	.	.	.	C	8.011	0.757438	0.15846	.	.	ENSG00000218672	ENST00000401499	.	.	.	1.65	0.706	0.18133	.	.	.	.	.	T	0.47764	0.1463	.	.	.	.	.	.	.	.	.	.	.	.	T	0.56613	-0.7950	4	0.87932	D	0	.	6.6695	0.23060	0.0:0.8161:0.0:0.1839	.	.	.	.	G	27	.	ENSP00000384676:A27G	A	+	2	0	AC008060.7	154867659	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.413000	0.07123	-0.092000	0.12417	-1.284000	0.01376	GCC			0.642	AC008060.7-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000322332.1			
FAM86B2	653333	bcgsc.ca	37	8	12287957	12287957	+	Missense_Mutation	SNP	C	C	T	rs148629503		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:12287957C>T	ENST00000262365.4	-	4	243	c.244G>A	c.(244-246)Gag>Aag	p.E82K	FAM86B2_ENST00000351291.4_Intron|FAM86B2_ENST00000309608.5_Intron|FAM86B2_ENST00000393715.3_Intron	NM_001137610.1	NP_001131082.1	P0C5J1	F86B2_HUMAN	family with sequence similarity 86, member B2	82										endometrium(1)|kidney(2)	3						TGGACAGCCTCGTGCTGGGGG	0.537																																					p.E82K													.	FAM86B2	19		0			c.G244A												13.0	16.0	15.0					8																	12287957		689	1588	2277	SO:0001583	missense	653333	exon4			CAGCCTCGTGCTG		CCDS59092.1	8p23.1	2011-07-01			ENSG00000145002	ENSG00000145002			32222	protein-coding gene	gene with protein product							Standard	NM_001137610		Approved		uc003wvt.4	P0C5J1	OTTHUMG00000165462	ENST00000262365.4:c.244G>A	8.37:g.12287957C>T	ENSP00000262365:p.Glu82Lys		296	0.0101351351	3		272	0.07	20	NM_001137610	0		0		Missense_Mutation	SNP	ENST00000262365.4	37	CCDS59092.1	.	.	.	.	.	.	.	.	.	.	-	13.25	2.180194	0.38511	.	.	ENSG00000145002	ENST00000262365	T	0.25414	1.8	1.16	1.16	0.20824	.	.	.	.	.	T	0.24661	0.0598	M	0.80982	2.52	0.80722	D	1	P	0.46395	0.877	B	0.36766	0.232	T	0.20940	-1.0260	9	0.72032	D	0.01	.	5.7399	0.18087	0.0:1.0:0.0:0.0	.	82	P0C5J1	F86B2_HUMAN	K	82	ENSP00000262365:E82K	ENSP00000262365:E82K	E	-	1	0	FAM86B2	12332328	0.994000	0.37717	0.994000	0.49952	0.123000	0.20343	2.765000	0.47621	0.945000	0.37605	0.162000	0.16502	GAG			0.537	FAM86B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				XM_928336	
Unknown	0	bcgsc.ca	37	8	13880224	13880224	+	IGR	SNP	G	G	A	rs4831261	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:13880224G>A								RP11-480O10.1 (173606 upstream) : SGCZ (67148 downstream)																							AGATGCGGCCGTATAATCTGA	0.398													A|||	875	0.17472	0.2897	0.0663	5008	,	,		19060	0.1875		0.1034	False		,,,				2504	0.1564				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCGGCCGTATAAT																													8.37:g.13880224G>A			140	0	0		119	0.08	9	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	8	13880562	13880562	+	IGR	SNP	G	G	T	rs7003822	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:13880562G>T								RP11-480O10.1 (173944 upstream) : SGCZ (66810 downstream)																							TTTCACGTAAGACAATCAACC	0.383													G|||	1159	0.23143	0.4584	0.1081	5008	,	,		15905	0.1746		0.1213	False		,,,				2504	0.184				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACGTAAGACAATC																													8.37:g.13880562G>T			230	0	0		151	0.13	19	.	0		0		RNA	SNP		37																																																																																					0	0.383										
PPM1AP1	137012	bcgsc.ca	37	8	15663805	15663805	+	IGR	SNP	C	C	A	rs73199378	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:15663805C>A								TUSC3 (39647 upstream) : RP11-77B22.2 (167018 downstream)																							AATGTGTACACCACATGGACT	0.458													C|||	603	0.120407	0.1309	0.085	5008	,	,		20171	0.1389		0.1233	False		,,,				2504	0.1094				.													.	.			0			.																																									SO:0001628	intergenic_variant	137012	.			TGTACACCACATG																													8.37:g.15663805C>A			70	0	0		56	0.11	6	.	0		0		RNA	SNP		37																																																																																					0	0.458										
TMEM97P2	724059	bcgsc.ca	37	8	20792070	20792070	+	IGR	SNP	G	G	C	rs11776249	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:20792070G>C								RP11-108E14.1 (234615 upstream) : RP11-369E15.1 (6868 downstream)																							TTCGAATCCAGTTGCAGCTTC	0.438													C|||	2903	0.579673	0.8306	0.5951	5008	,	,		19001	0.2371		0.5417	False		,,,				2504	0.6217				.													.	.			0			.																																									SO:0001628	intergenic_variant	724059	.			AATCCAGTTGCAG																													8.37:g.20792070G>C			45	0	0		55	0.20	11	.	0		0		RNA	SNP		37																																																																																					0	0.438										
C8orf58	541565	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	22459522	22459522	+	Missense_Mutation	SNP	C	C	T	rs147143680		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:22459522C>T	ENST00000289989.5	+	4	769	c.695C>T	c.(694-696)cCg>cTg	p.P232L	C8orf58_ENST00000409586.3_Missense_Mutation_p.P232L|CCAR2_ENST00000521301.1_5'Flank|CCAR2_ENST00000308511.4_5'Flank			Q8NAV2	CH058_HUMAN	chromosome 8 open reading frame 58	232										endometrium(1)|lung(1)|ovary(1)|skin(1)	4		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00563)|Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GCCCCTTTACCGTCCCCGTTA	0.637																																					p.P232L													.	.			0			c.C695T								LEU/PRO,LEU/PRO,LEU/PRO	0,4378		0,0,2189	32.0	29.0	30.0		695,695,695	-0.1	0.0	8	dbSNP_134	30	1,8591		0,1,4295	no	missense,missense,missense	C8orf58	NM_001013842.2,NM_001198827.1,NM_173686.2	98,98,98	0,1,6484	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	232/366,232/301,232/358	22459522	1,12969	2189	4296	6485	SO:0001583	missense	541565	exon4			CTTTACCGTCCCC	BC012750	CCDS34862.1, CCDS56527.1, CCDS75708.1	8p21.3	2010-08-17			ENSG00000241852	ENSG00000241852			32233	protein-coding gene	gene with protein product							Standard	NM_001013842		Approved	FLJ34715	uc003xce.3	Q8NAV2	OTTHUMG00000154160	ENST00000289989.5:c.695C>T	8.37:g.22459522C>T	ENSP00000289989:p.Pro232Leu		111	0	0		108	0.26	28	NM_001013842	57	0.32	18	B4DI44	Missense_Mutation	SNP	ENST00000289989.5	37	CCDS34862.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	5.222|5.222	0.226547|0.226547	0.09916|0.09916	0.0|0.0	1.16E-4|1.16E-4	ENSG00000248235;ENSG00000241852;ENSG00000241852;ENSG00000241852;ENSG00000241852|ENSG00000241852	ENST00000450780;ENST00000409586;ENST00000289989;ENST00000381191;ENST00000475994|ENST00000495957	.|.	.|.	.|.	3.72|3.72	-0.127|-0.127	0.13510|0.13510	.|.	0.866804|.	0.09800|.	N|.	0.754216|.	T|T	0.15089|0.15089	0.0364|0.0364	N|N	0.11201|0.11201	0.11|0.11	0.09310|0.09310	N|N	1|1	B;B;B|.	0.19331|.	0.035;0.035;0.035|.	B;B;B|.	0.15052|.	0.006;0.012;0.007|.	T|T	0.24261|0.24261	-1.0165|-1.0165	9|5	0.05959|.	T|.	0.93|.	0.5223|0.5223	2.9911|2.9911	0.05983|0.05983	0.1935:0.4796:0.0:0.327|0.1935:0.4796:0.0:0.327	.|.	232;160;232|.	Q8NAV2-2;E7EQH9;Q8NAV2|.	.;.;CH058_HUMAN|.	L|C	301;232;232;160;31|3	.|.	ENSP00000399696:P301L|.	P|R	+|+	2|1	0|0	AC037459.4;C8orf58|C8orf58	22515467|22515467	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.556000|-0.556000	0.05992|0.05992	-0.054000|-0.054000	0.13266|0.13266	-0.461000|-0.461000	0.05368|0.05368	CCG|CGT	0		0.637	C8orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000334183.1		NM_001013842	
MAP2K1P1	29778	bcgsc.ca	37	8	29885662	29885662	+	IGR	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:29885662G>A								MIR3148 (70798 upstream) : RNU6-1218P (15654 downstream)																							GTATCTGCAGGTAGCACATGG	0.463																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	29778	.			CTGCAGGTAGCAC																													8.37:g.29885662G>A			85	0	0		70	0.13	9	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.463										
MAP2K1P1	29778	bcgsc.ca	37	8	29886264	29886264	+	IGR	DEL	A	A	-	rs397771909|rs34759986	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:29886264delA								MIR3148 (71400 upstream) : RNU6-1218P (15052 downstream)																							AATGCCTAATAAAAACCCCGT	0.423													?|AAAAA|AAAA|unsure	1640	0.327476	0.1188	0.5403	5008	,	,		19296	0.2044		0.5348	False		,,,				2504	0.3722				.													.	.			0			.																																									SO:0001628	intergenic_variant	29778	.			CCTAATAAAAACC																													8.37:g.29886264delA			77	0	0		79	0.20	16	.	3	0.00	0		RNA	DEL		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	8	30841331	30841331	+	IGR	SNP	C	C	T	rs2080720	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:30841331C>T								TEX15 (95109 upstream) : PURG (11989 downstream)																							GTATCTATTACCCACTGGAGG	0.398													T|||	3698	0.738419	0.8215	0.7392	5008	,	,		19566	0.9494		0.6203	False		,,,				2504	0.5297				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTATTACCCACTG																													8.37:g.30841331C>T			40	0	0		35	0.26	9	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	8	30841522	30841522	+	IGR	SNP	A	A	G	rs199721137|rs386724128|rs34384747|rs2344121	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:30841522A>G								TEX15 (95300 upstream) : PURG (11798 downstream)																							TTCCTGAGGAAGCCCCTTTCT	0.388													A|||	1863	0.372005	0.0363	0.4323	5008	,	,		19439	0.6825		0.505	False		,,,				2504	0.3262				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGAGGAAGCCCCT																													8.37:g.30841522A>G			63	0	0		55	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.388										
SDR16C6P	442388	broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	57294571	57294571	+	RNA	SNP	C	C	G	rs10216409	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:57294571C>G	ENST00000517787.1	-	0	337					NR_103832.1				short chain dehydrogenase/reductase family 16C, member 6, pseudogene																		CACGATGGTGCTTTTAACTTC	0.343													G|||	2118	0.422923	0.5303	0.5029	5008	,	,		15510	0.373		0.325	False		,,,				2504	0.3732				.													.	.			0			.							G		693,691		173,347,172	96.0	83.0	87.0			3.1	0.9	8	dbSNP_119	87	989,2193		161,667,763	no	intergenic				334,1014,935	GG,GC,CC		31.0811,49.9277,36.8375			57294571	1682,2884	692	1591	2283			0	.			ATGGTGCTTTTAA			8q12.1	2011-09-20	2010-12-20	2010-12-20	ENSG00000253542	ENSG00000253542		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	35413	pseudogene	pseudogene			"""short chain dehydrogenase/reductase family 16C, member 6"""	SDR16C6		19027726	Standard	NR_103832		Approved				OTTHUMG00000164408		8.37:g.57294571C>G			166	0.0060240964	1		120	0.18	21	.	0		0		RNA	SNP	ENST00000517787.1	37																																																																																						0.343	SDR16C6P-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000378641.3			
AC022182.1	0	bcgsc.ca	37	8	61851466	61851466	+	lincRNA	SNP	T	T	C	rs3748648	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:61851466T>C	ENST00000527672.1	+	0	323																											GAGTCTGATCTCCTACAGCTG	0.502													T|||	1295	0.258586	0.1452	0.5317	5008	,	,		21112	0.2123		0.4115	False		,,,				2504	0.1084				.													.	.			0			.																																											0	.			CTGATCTCCTACA																													8.37:g.61851466T>C			189	0	0		168	0.05	9	.	1	0.00	0		RNA	SNP	ENST00000527672.1	37																																																																																						0.502	AC022182.1-002	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000383484.1			
Unknown	0	bcgsc.ca	37	8	70042263	70042263	+	IGR	SNP	A	A	G	rs67905920	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:70042263A>G								RNU7-102P (19454 upstream) : RP11-21C17.1 (45550 downstream)																							AGGAGCGTGCAGAGATGCGTG	0.512													a|||	2740	0.547125	0.8207	0.487	5008	,	,		19347	0.5427		0.3946	False		,,,				2504	0.3814				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCGTGCAGAGATG																													8.37:g.70042263A>G			57	0	0		50	0.18	9	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.512										
Unknown	0	bcgsc.ca	37	8	88801868	88801868	+	IGR	SNP	T	T	G	rs16873107	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:88801868T>G								AF121898.3 (33922 upstream) : DCAF4L2 (81104 downstream)																							CCATCAGAGGTCTTGGGTTTG	0.498													T|||	1160	0.231629	0.1172	0.3963	5008	,	,		17202	0.4107		0.1839	False		,,,				2504	0.1339				.													.	.			0			.																																									SO:0001628	intergenic_variant	6661	.			CAGAGGTCTTGGG																													8.37:g.88801868T>G			93	0.0107526882	1		84	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.498										
FAM83A	84985	bcgsc.ca	37	8	124221677	124221681	+	3'UTR	DEL	AAACA	AAACA	-			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AAACA	AAACA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:124221677_124221681delAAACA	ENST00000518448.1	+	0	5068_5072				FAM83A_ENST00000276699.6_Frame_Shift_Del_p.KQ349fs|FAM83A_ENST00000546351.1_Intron|FAM83A_ENST00000536633.1_Frame_Shift_Del_p.KQ349fs|FAM83A_ENST00000522648.1_Intron			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TCCTGAAAGTAAACAAAACAAAACA	0.366																																					p.349_350del													.	FAM83A	64		0			c.1045_1049del																																									SO:0001624	3_prime_UTR_variant	84985	exon5			GAAAGTAAACAAA	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.*1753AAACA>-	8.37:g.124221687_124221691delAAACA			92	0	0		97	0.03	3	NM_207006	0		0	Q71HL2|Q8N7I1|Q96I47	Frame_Shift_Del	DEL	ENST00000518448.1	37	CCDS6340.1																																																																																					0.366	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000381737.1		NM_032899	
LINC00964	157381	bcgsc.ca	37	8	125933052	125933052	+	IGR	SNP	T	T	C	rs17395997	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:125933052T>C								RP11-1082L8.3 (63294 upstream) : RP11-1082L8.2 (15713 downstream)																							GTAATTTAAATTTAGAGCAAT	0.413													C|||	2702	0.539537	0.6135	0.3963	5008	,	,		18433	0.381		0.6113	False		,,,				2504	0.6309				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTAAATTTAGAG																													8.37:g.125933052T>C			108	0.0092592593	1		66	0.11	7	.	0		0		RNA	SNP		37																																																																																					0	0.413										
LOC101928087	101928087	bcgsc.ca	37	8	143719983	143719983	+	RNA	SNP	G	G	C	rs2280881	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr8:143719983G>C	ENST00000522374.1	+	0	35																											TGGCCATGACGCCAGTGGCCA	0.632													C|||	2304	0.460064	0.553	0.2896	5008	,	,		15770	0.4871		0.3519	False		,,,				2504	0.5389				.													.	.			0			.																																											0	.			CATGACGCCAGTG																													8.37:g.143719983G>C			179	0	0		180	0.10	18	.	0		0		RNA	SNP	ENST00000522374.1	37																																																																																						0.632	AC145123.2-001	KNOWN	basic|exp_conf	antisense	antisense		OTTHUMT00000380518.1			
RNF2P1	100132467	bcgsc.ca	37	9	6669375	6669375	+	lincRNA	SNP	C	C	G	rs2297556	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:6669375C>G	ENST00000413145.1	+	0	130																											TCCATTGCTGCATTGTTATTA	0.418													C|||	1345	0.26857	0.2027	0.3329	5008	,	,		24312	0.3889		0.1491	False		,,,				2504	0.3108				.													.	.			0			.																																											100132467	.			TTGCTGCATTGTT																													9.37:g.6669375C>G			74	0	0		65	0.11	7	.	0		0		RNA	SNP	ENST00000413145.1	37																																																																																						0.418	RP11-390F4.6-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000051688.1			
ME2P1	286239	bcgsc.ca	37	9	29826486	29826486	+	IGR	SNP	G	G	A	rs79694178	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:29826486G>A								MIR873 (937533 upstream) : snoU13 (351986 downstream)																							TGGAAACTACGCTTAACCCGG	0.502													g|||	108	0.0215655	0.003	0.0231	5008	,	,		15278	0.0		0.0646	False		,,,				2504	0.0235				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AACTACGCTTAAC																													9.37:g.29826486G>A			34	0	0		30	0.17	5	.	0		0		RNA	SNP		37																																																																																					0	0.502										
RBMXP2	441391	bcgsc.ca	37	9	30689445	30689445	+	IGR	SNP	G	G	A	rs200326968		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:30689445G>A								snoU13 (510870 upstream) : AL590726.2 (81649 downstream)																							TGGAAGAGGAGGAAGTGGAGG	0.522																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			AGAGGAGGAAGTG																													9.37:g.30689445G>A			492	0	0		443	0.04	18	.	37	0.00	0		RNA	SNP		37																																																																																					0	0.522										
RBMXP2	441391	bcgsc.ca	37	9	30689459	30689459	+	IGR	SNP	A	A	C	rs201295283		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:30689459A>C								snoU13 (510884 upstream) : AL590726.2 (81635 downstream)																							GTGGAGGAACAAGGGGACCTC	0.512																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			AGGAACAAGGGGA																													9.37:g.30689459A>C			483	0	0		430	0.05	20	.	4	0.50	2		RNA	SNP		37																																																																																					0	0.512										
RBMXP2	441391	bcgsc.ca	37	9	30690005	30690005	+	IGR	SNP	A	A	C	rs78196531		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:30690005A>C								snoU13 (511430 upstream) : AL590726.2 (81089 downstream)																							GAGGGCCCCCACCATCTTATG	0.483																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			GCCCCCACCATCT																													9.37:g.30690005A>C			276	0.0036231884	1		233	0.06	15	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	9	40610136	40610136	+	IGR	SNP	G	G	A	rs3739627		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:40610136G>A								RN7SL422P (93072 upstream) : SPATA31A3 (90154 downstream)																							AGGCCAGTGGGGCATCACAGT	0.478																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGTGGGGCATCA																													9.37:g.40610136G>A			577	0.0017331023	1		405	0.05	22	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.478										
CNTNAP3B	728577	bcgsc.ca	37	9	43822686	43822686	+	Missense_Mutation	SNP	C	C	A	rs62555055		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:43822686C>A	ENST00000377564.3	+	8	1633	c.1240C>A	c.(1240-1242)Cgt>Agt	p.R414S		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	414	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.			R -> S (in Ref. 1; BAB70782). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						CGAACTTCAACGTGGTTCAGG	0.502																																					p.R414S													.	CNTNAP3B	37		0			c.C1240A																																									SO:0001583	missense	728577	exon8			CTTCAACGTGGTT	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.1240C>A	9.37:g.43822686C>A	ENSP00000366787:p.Arg414Ser		298	0.0067114094	2		235	0.11	25	NM_001201380	0		0	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.827|8.827	0.939072|0.939072	0.18281|0.18281	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377561|ENST00000377564;ENST00000341990;ENST00000403166	.|T	.|0.77877	.|-1.13	2.83|2.83	1.91|1.91	0.25777|0.25777	.|.	.|.	.|.	.|.	.|.	T|T	0.57051|0.57051	0.2027|0.2027	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55036|0.55036	-0.8203|-0.8203	4|6	.|0.07990	.|T	.|0.79	.|.	8.6249|8.6249	0.33883|0.33883	0.0:0.8775:0.0:0.1225|0.0:0.8775:0.0:0.1225	.|.	.|.	.|.	.|.	K|S	462|414	.|ENSP00000366787:R414S	.|ENSP00000340890:R414S	N|R	+|+	3|1	2|0	CNTNAP3B|CNTNAP3B	43762682|43762682	0.004000|0.004000	0.15560|0.15560	0.004000|0.004000	0.12327|0.12327	0.319000|0.319000	0.28217|0.28217	1.982000|1.982000	0.40638|0.40638	0.514000|0.514000	0.28300|0.28300	0.423000|0.423000	0.28283|0.28283	AAC|CGT			0.502	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000036930.3			
CNTNAP3B	728577	bcgsc.ca	37	9	43822704	43822704	+	Missense_Mutation	SNP	G	G	A	rs62555056		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:43822704G>A	ENST00000377564.3	+	8	1651	c.1258G>A	c.(1258-1260)Gtc>Atc	p.V420I		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	420	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.			V -> I (in Ref. 1; BAB70782). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						AGGGAGTTTCGTCCTCTTTCT	0.478																																					p.V420I													.	CNTNAP3B	37		0			c.G1258A																																									SO:0001583	missense	728577	exon8			AGTTTCGTCCTCT	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.1258G>A	9.37:g.43822704G>A	ENSP00000366787:p.Val420Ile		301	0	0		236	0.09	22	NM_001201380	0		0	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	G	6.568	0.473072	0.12461	.	.	ENSG00000154529	ENST00000377564;ENST00000341990;ENST00000403166	T	0.77620	-1.11	2.66	-5.32	0.02722	.	.	.	.	.	T	0.64091	0.2567	L	0.29908	0.895	0.80722	P	0.0	.	.	.	.	.	.	T	0.57883	-0.7734	6	0.22109	T	0.4	.	9.5395	0.39242	0.1327:0.5788:0.2884:0.0	.	.	.	.	I	420	ENSP00000366787:V420I	ENSP00000340890:V420I	V	+	1	0	CNTNAP3B	43762700	0.001000	0.12720	0.004000	0.12327	0.327000	0.28475	-1.620000	0.02046	-1.150000	0.02840	-0.717000	0.03617	GTC			0.478	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000036930.3			
DPP3P2	138971	bcgsc.ca	37	9	76089841	76089841	+	IGR	SNP	C	C	A	rs278746	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:76089841C>A								AL449083.1 (183698 upstream) : RP11-128I7.1 (98689 downstream)																							CCAGAGCGAGCAGCCCAGCCC	0.597													C|||	452	0.0902556	0.2474	0.0317	5008	,	,		18020	0.005		0.0408	False		,,,				2504	0.0583				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGCGAGCAGCCCA																													9.37:g.76089841C>A			36	0	0		31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.597										
Unknown	0	bcgsc.ca	37	9	80834173	80834173	+	IGR	SNP	A	A	G	rs878922	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:80834173A>G								RN7SKP59 (53479 upstream) : CEP78 (16804 downstream)																							GAGGAGACTTATGTCCAATGG	0.448													G|||	3364	0.671725	0.7065	0.6254	5008	,	,		19554	0.7897		0.5318	False		,,,				2504	0.68				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGACTTATGTCCA																													9.37:g.80834173A>G			110	0.0090909091	1		101	0.17	17	.	0		0		RNA	SNP		37																																																																																					0	0.448										
RP11-213G2.2	0	bcgsc.ca	37	9	88401021	88401021	+	lincRNA	SNP	A	A	G	rs11141102	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:88401021A>G	ENST00000443630.1	-	0	386																											TTTAGATCATAAGGCTGGAGA	0.333													G|||	555	0.110823	0.0295	0.1628	5008	,	,		17331	0.0506		0.2087	False		,,,				2504	0.1452				.													.	.			0			.																																											0	.			GATCATAAGGCTG																													9.37:g.88401021A>G			253	0.0039525692	1		208	0.07	15	.	0		0		RNA	SNP	ENST00000443630.1	37																																																																																						0.333	RP11-213G2.2-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000052899.1			
RP13-60M5.2	0	bcgsc.ca	37	9	91262493	91262494	+	lincRNA	DNP	AG	AG	CT	rs386736063|rs72751473|rs72751474	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:91262493_91262494AG>CT	ENST00000418343.2	-	0	257_258																											ACACATTTCCAGGTCTCAGCAG	0.396																																					.													.	.			0			c.C149A																																											0	exon2			ATTTCCAGGTCTC																												Exception_encountered	9.37:g.91262493_91262494delinsCT			144	0.0069444444	1		138	0.06	8	NM_001100111	0		0		RNA	DNP	ENST00000418343.2	37																																																																																						0.396	RP13-60M5.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000052976.2			
RP13-60M5.2	0	bcgsc.ca	37	9	91262522	91262522	+	lincRNA	SNP	T	T	A	rs28429833	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:91262522T>A	ENST00000418343.2	-	0	229																											GGGGTTGGATTAAGCACCATG	0.403													T|||	1014	0.202476	0.2958	0.2248	5008	,	,		21739	0.1706		0.164	False		,,,				2504	0.1329				p.N41Y													.	.			0			c.A121T							T	TYR/ASN	1005,2875		135,735,1070	155.0	143.0	147.0		121	-0.7	0.0	9	dbSNP_125	147	1296,6972		97,1102,2935	yes	missense	LOC286238	NM_001100111.1	143	232,1837,4005	AA,AT,TT		15.6749,25.9021,18.9414		41/113	91262522	2301,9847	1940	4134	6074			0	exon2			TTGGATTAAGCAC																													9.37:g.91262522T>A			149	0	0		131	0.05	7	NM_001100111	0		0		RNA	SNP	ENST00000418343.2	37																																																																																						0.403	RP13-60M5.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000052976.2			
ANKRD18CP	100287922	bcgsc.ca	37	9	99983312	99983312	+	IGR	SNP	C	C	T	rs12235734	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:99983312C>T								RP11-498P14.3 (23343 upstream) : RP11-498P14.4 (12170 downstream)																							CCCCCGCTACCTGTCCTTTCT	0.731													C|||	1796	0.358626	0.2398	0.2795	5008	,	,		11446	0.3671		0.504	False		,,,				2504	0.4172				.													.	.			0			.																																									SO:0001628	intergenic_variant	100287922	.			CGCTACCTGTCCT																													9.37:g.99983312C>T			45	0	0		42	0.14	6	.	0		0		RNA	SNP		37																																																																																					0	0.731										
LAMC3	10319	bcgsc.ca	37	9	133901819	133901820	+	Missense_Mutation	DNP	CC	CC	AG	rs2275136|rs386738954|rs2275137	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:133901819_133901820CC>AG	ENST00000361069.4	+	2	654_655	c.521_522CC>AG	c.(520-522)cCC>cAG	p.P174Q	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	174	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		TACGGCCGGCCCGAGGGCCAGT	0.678																																					p.P174Q													.	LAMC3	167		0			c.C522G																																									SO:0001583	missense	10319	exon2			GCCGGCCCGAGGG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	Exception_encountered	9.37:g.133901819_133901820delinsAG	ENSP00000354360:p.Pro174Gln		188	0	0		170	0.04	6	NM_006059	72	0.00	0	B1APX9|B1APY0|Q59H72	Missense_Mutation	DNP	ENST00000361069.4	37	CCDS6938.1																																																																																					0.678	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000054717.3		NM_006059	
SOCS5P2	100128299	bcgsc.ca	37	9	138340462	138340462	+	IGR	SNP	A	A	G	rs10732637	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:138340462A>G								RP11-555H7.2 (94396 upstream) : PPP1R26-AS1 (14110 downstream)																							TGAAGAAGGGATAGATCCCCC	0.413													G|||	3836	0.765974	0.9009	0.8199	5008	,	,		19988	0.5794		0.7883	False		,,,				2504	0.7147				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAAGGGATAGATC																													9.37:g.138340462A>G			41	0	0		32	0.31	10	.	0		0		RNA	SNP		37																																																																																					0	0.413										
Unknown	0	bcgsc.ca	37	9	141035935	141035935	+	IGR	SNP	T	T	C	rs115489568		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:141035935T>C								CACNA1B (16859 upstream) : TUBBP5 (8629 downstream)																							GTGCCCTCTCTAGCAGTGTTC	0.597																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTCTCTAGCAGT																													9.37:g.141035935T>C			51	0	0		80	0.11	9	.	0		0		RNA	SNP		37																																																																																					0	0.597										
Unknown	0	bcgsc.ca	37	9	141038257	141038257	+	IGR	SNP	T	T	G	rs2507153		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:141038257T>G								CACNA1B (19181 upstream) : TUBBP5 (6307 downstream)																							CAGGAGGACTTGGCCCCCACG	0.607																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGACTTGGCCCC																													9.37:g.141038257T>G			29	0	0		36	0.14	5	.	0		0		RNA	SNP		37																																																																																					0	0.607										
Unknown	0	bcgsc.ca	37	9	141038277	141038277	+	IGR	SNP	A	A	G	rs28521831		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chr9:141038277A>G								CACNA1B (19201 upstream) : TUBBP5 (6287 downstream)																							GTCCCCCACCAGGGCATGTTA	0.577																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCCACCAGGGCAT																													9.37:g.141038277A>G			23	0	0		30	0.20	6	.	0		0		RNA	SNP		37																																																																																					0	0.577										
PTCHD1-AS	100873065	bcgsc.ca	37	X	22454639	22454639	+	lincRNA	SNP	C	C	T	rs7391306		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:22454639C>T	ENST00000455399.1	-	0	312				RP11-494I9.2_ENST00000456621.1_lincRNA																							TCAGAAGTTTCTGAGACCTGG	0.428													.|||	467	0.123709	0.0189	0.1441	3775	,	,		16266	0.0536		0.1382	False		,,,				2504	0.1524				.													.	.			0			.																																											729650	.			AAGTTTCTGAGAC																													X.37:g.22454639C>T			100	0	0		98	0.05	5	.	0		0		RNA	SNP	ENST00000455399.1	37																																																																																						0.428	RP11-40F8.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000056044.1			
ARX	170302	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	X	25031217	25031217	+	Missense_Mutation	SNP	G	G	A			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:25031217G>A	ENST00000379044.4	-	2	1105	c.895C>T	c.(895-897)Ccg>Tcg	p.P299S		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox	299					axon guidance (GO:0007411)|cell proliferation in forebrain (GO:0021846)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex tangential migration (GO:0021800)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|epithelial cell fate commitment (GO:0072148)|globus pallidus development (GO:0021759)|lipid digestion (GO:0044241)|positive regulation of organ growth (GO:0046622)|regulation of cell proliferation (GO:0042127)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			kidney(1)|large_intestine(2)|lung(1)	4						GCGTCTTCCGGGTGCAGCAGC	0.697																																					p.P299S													.	.			0			c.C895T												24.0	18.0	20.0					X																	25031217		2201	4298	6499	SO:0001583	missense	170302	exon2			CTTCCGGGTGCAG	AY038071	CCDS14215.1	Xp21.3	2011-06-20			ENSG00000004848	ENSG00000004848		"""Homeoboxes / PRD class"""	18060	protein-coding gene	gene with protein product	"""cancer/testis antigen 121"""	300382	"""mental retardation, X-linked 54"", ""mental retardation, X-linked 43"", ""mental retardation, X-linked 36"", ""mental retardation, X-linked 29"", ""mental retardation, X-linked 32"", ""mental retardation, X-linked 33"", ""mental retardation, X-linked 38"", ""mental retardation, X-linked 87"", ""mental retardation, X-linked 76"""	MRXS1, PRTS, MRX76, MRX54, MRX43, MRX36, MRX29, MRX32, MRX33, MRX38, MRX87		11889467, 15850492, 17480217	Standard	NM_139058		Approved	ISSX, CT121, EIEE1	uc004dbp.4	Q96QS3	OTTHUMG00000021275	ENST00000379044.4:c.895C>T	X.37:g.25031217G>A	ENSP00000368332:p.Pro299Ser		67	0	0		90	0.47	42	NM_139058	2	0.50	1		Missense_Mutation	SNP	ENST00000379044.4	37	CCDS14215.1	.	.	.	.	.	.	.	.	.	.	g	2.759	-0.258267	0.05791	.	.	ENSG00000004848	ENST00000379044	D	0.93953	-3.32	3.83	3.83	0.44106	.	0.160952	0.41938	U	0.000787	D	0.82440	0.5037	N	0.08118	0	0.32790	N	0.501298	B	0.15930	0.015	B	0.12156	0.007	T	0.77547	-0.2547	10	0.13470	T	0.59	.	9.0679	0.36475	0.11:0.0:0.89:0.0	.	299	Q96QS3	ARX_HUMAN	S	299	ENSP00000368332:P299S	ENSP00000368332:P299S	P	-	1	0	ARX	24941138	1.000000	0.71417	0.997000	0.53966	0.451000	0.32288	3.138000	0.50570	1.518000	0.48934	0.141000	0.15989	CCG			0.697	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056109.1			
MAGEB16	139604	ucsc.edu	37	X	35821055	35821056	+	Missense_Mutation	DNP	AT	AT	GA	rs4829391|rs4829390|rs370444095	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:35821055_35821056AT>GA	ENST00000399989.1	+	2	1021_1022	c.742_743AT>GA	c.(742-744)ATg>GAg	p.M248E	MAGEB16_ENST00000399987.1_Missense_Mutation_p.M248E|MAGEB16_ENST00000399992.1_Missense_Mutation_p.M280E|MAGEB16_ENST00000399985.1_Missense_Mutation_p.M248E|MAGEB16_ENST00000399988.1_Missense_Mutation_p.M248E	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	248	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		M -> K (in dbSNP:rs4829391).|M -> V (in dbSNP:rs4829390).							breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						AGAGCCCAGAATGCTCATCACC	0.505																																					p.M280E													.	MAGEB16	64		0			c.T743A																																									SO:0001583	missense	139604	exon2			CCCAGAATGCTCA		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	Exception_encountered	X.37:g.35821055_35821056delinsGA	ENSP00000382871:p.Met248Glu		163	0.018404908	3		171	0.12	20	NM_001099921	0		0	A8MU30	Missense_Mutation	DNP	ENST00000399989.1	37	CCDS43927.1																																																																																					0.505	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000251034.1			
KDM6A	7403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	44918601	44918602	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	TA	TA					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:44918601_44918602delTA	ENST00000377967.4	+	12	1125_1126	c.1084_1085delTA	c.(1084-1086)tatfs	p.Y362fs	KDM6A_ENST00000543216.1_Frame_Shift_Del_p.Y362fs|KDM6A_ENST00000536777.1_Frame_Shift_Del_p.Y362fs|KDM6A_ENST00000382899.4_Frame_Shift_Del_p.Y362fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	362	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)|p.0(2)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AGGCACTCTCTATGAATCCTGC	0.455			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																p.361_362del	Colon(129;1273 1667 15230 27352 52914)			Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274		8	Whole gene deletion(6)|No detectable mRNA/protein(2)	haematopoietic_and_lymphoid_tissue(2)|oesophagus(2)|breast(2)|pancreas(2)	c.1083_1084del																																									SO:0001589	frameshift_variant	7403	exon12			ACTCTCTATGAAT	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.1084_1085delTA	X.37:g.44918601_44918602delTA	ENSP00000367203:p.Tyr362fs		228	0	0		216	0.00	0	NM_021140	19	0.00	0	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																					0.455	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056324.1		NM_021140	
XAGE-4	139629	bcgsc.ca	37	X	55683421	55683421	+	RNA	SNP	A	A	G	rs187148944		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:55683421A>G	ENST00000513415.1	-	0	0																											GTCTAGGCCTATATGTTGATC	0.403													A|||	13	0.00344371	0.0083	0.0014	3775	,	,		15510	0.001		0.0	False		,,,				2504	0.0				.													.	.			0			.																																											0	.			AGGCCTATATGTT																													X.37:g.55683421A>G			105	0	0		141	0.04	6	.	0		0		RNA	SNP	ENST00000513415.1	37																																																																																						0.403	RP11-167P23.2-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000367028.1			
Unknown	0	bcgsc.ca	37	X	65176531	65176531	+	IGR	SNP	T	T	C	rs199968155		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:65176531T>C								MSN (214740 upstream) : RP6-159A1.3 (43061 downstream)																							TGCGAACTGGTCCTGAAGGTG	0.512																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AACTGGTCCTGAA																													X.37:g.65176531T>C			217	0	0		309	0.06	17	.	81	0.00	0		RNA	SNP		37																																																																																					0	0.512										
Unknown	0	bcgsc.ca	37	X	65176539	65176539	+	IGR	SNP	G	G	C	rs112831485	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:65176539G>C								MSN (214748 upstream) : RP6-159A1.3 (43053 downstream)																							GGTCCTGAAGGTGCAGATCTC	0.507																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGAAGGTGCAGA																													X.37:g.65176539G>C			233	0	0		317	0.06	18	.	55	0.00	0		RNA	SNP		37																																																																																					0	0.507										
FAM155B	27112	ucsc.edu	37	X	68749750	68749750	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:68749750G>T	ENST00000252338.4	+	3	1412	c.1370G>T	c.(1369-1371)gGg>gTg	p.G457V		NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	458	Poly-Gly.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						GGGGGATTGGGGCTGGAGACA	0.622																																					p.G457V													.	FAM155B	44		0			c.G1370T												46.0	33.0	37.0					X																	68749750		2203	4299	6502	SO:0001583	missense	27112	exon3			GATTGGGGCTGGA	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"""transmembrane protein 28"", ""chromosome X open reading frame 63"""	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.1370G>T	X.37:g.68749750G>T	ENSP00000252338:p.Gly457Val		56	0	0		54	0.09	5	NM_015686	50	0.00	0	B1ALV6|B9EGK1|D3DVU1	Missense_Mutation	SNP	ENST00000252338.4	37	CCDS35317.1	.	.	.	.	.	.	.	.	.	.	G	12.26	1.885125	0.33255	.	.	ENSG00000130054	ENST00000252338	T	0.54279	0.58	4.23	3.36	0.38483	.	0.158012	0.39407	N	0.001375	T	0.62600	0.2441	L	0.52573	1.65	0.58432	D	0.999997	D	0.89917	1.0	D	0.72338	0.977	T	0.62637	-0.6812	10	0.72032	D	0.01	-9.2052	8.8925	0.35444	0.115:0.0:0.885:0.0	.	457	O75949-2	.	V	457	ENSP00000252338:G457V	ENSP00000252338:G457V	G	+	2	0	FAM155B	68666475	1.000000	0.71417	0.996000	0.52242	0.639000	0.38242	4.796000	0.62496	0.804000	0.34136	0.411000	0.27672	GGG			0.622	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000057037.1		NM_015686	
USP12PX	254700	bcgsc.ca	37	X	89367831	89367831	+	IGR	SNP	C	C	T	rs111832781		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:89367831C>T								TGIF2LX (189949 upstream) : RNU6-555P (484402 downstream)																							TTTTGTCGTCCGTTTCGGGAA	0.408													C|||	41	0.0108609	0.0008	0.0014	3775	,	,		12910	0.0198		0.0089	False		,,,				2504	0.0102				.													.	.			0			.																																									SO:0001628	intergenic_variant	254700	.			GTCGTCCGTTTCG																													X.37:g.89367831C>T			32	0	0		36	0.17	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.408										
USP12PX	254700	bcgsc.ca	37	X	89368160	89368160	+	IGR	SNP	G	G	A	rs112135433		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:89368160G>A								TGIF2LX (190278 upstream) : RNU6-555P (484073 downstream)																							CCCAACGTGGGTTCATGAGAT	0.358													G|||	7	0.0018543	0.0	0.0014	3775	,	,		13674	0.0		0.006	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	254700	.			ACGTGGGTTCATG																													X.37:g.89368160G>A			78	0	0		84	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.358										
Unknown	0	bcgsc.ca	37	X	99405357	99405357	+	IGR	SNP	T	T	C	rs5967081	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:99405357T>C								SNORA25 (50138 upstream) : PCDH19 (141284 downstream)																							GAAGAACAGATTTCCTATTTA	0.423													t|||	596	0.157881	0.1263	0.1599	3775	,	,		14131	0.0308		0.2336	False		,,,				2504	0.0532				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AACAGATTTCCTA																													X.37:g.99405357T>C			62	0	0		86	0.13	11	.	0		0		RNA	SNP		37																																																																																					0	0.423										
FRMPD3	84443	bcgsc.ca	37	X	106846552	106846552	+	Silent	SNP	G	G	A	rs141655380		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:106846552G>A	ENST00000276185.4	+	16	5382	c.5382G>A	c.(5380-5382)tcG>tcA	p.S1794S				Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	1794						cytoskeleton (GO:0005856)		p.S1843S(1)|p.S1794S(1)		breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(16)|ovary(2)|urinary_tract(1)	28						CCCCAACTTCGGCGACTGTTA	0.567													g|||	141	0.037351	0.1036	0.0058	3775	,	,		14048	0.0		0.0	False		,,,				2504	0.0				.													.	.			2	Substitution - coding silent(2)	breast(2)	.												2.0	2.0	2.0					X																	106846552		539	1224	1763	SO:0001819	synonymous_variant	84443	.			AACTTCGGCGACT	AB058720	CCDS76006.1	Xq22	2008-02-05			ENSG00000147234	ENSG00000147234			29382	protein-coding gene	gene with protein product						11347906	Standard	NM_032428		Approved	RP5-1070B1.1, KIAA1817		Q5JV73	OTTHUMG00000022165	ENST00000276185.4:c.5382G>A	X.37:g.106846552G>A			266	0	0		244	0.03	8	.	2	0.00	0	Q96JK8	Silent	SNP	ENST00000276185.4	37																																																																																						0.567	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
MRRFP1	286423	bcgsc.ca	37	X	122250996	122250996	+	IGR	SNP	G	G	T	rs6648942	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:122250996G>T								U3 (276499 upstream) : GRIA3 (67009 downstream)																							TAAAGAGTATGTGGCCTTGTT	0.468													T|||	2076	0.549934	0.3631	0.4769	3775	,	,		16291	0.5635		0.2008	False		,,,				2504	0.5061				.													.	.			0			.																																									SO:0001628	intergenic_variant	286423	.			GAGTATGTGGCCT																													X.37:g.122250996G>T			243	0.0041152263	1		230	0.07	16	.	1	0.00	0		Missense_Mutation	SNP		37		808	0.487040385774563	122	0.3193717277486911	98	0.3656716417910448	217	0.5896739130434783	119	0.1803030303030303	T	6.412	0.444056	0.12164	.	.	ENSG00000224236	ENST00000435941	.	.	.	1.49	1.49	0.22878	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.46345	-0.9198	5	0.02654	T	1	-1.3317	5.4932	0.16787	0.0:0.0:0.2846:0.7154	rs6648942;rs16997095;rs52801655;rs56738867;rs6648942	.	.	.	K	205	.	ENSP00000387841:T205K	T	-	2	0	MRRFP1	122078677	1.000000	0.71417	0.164000	0.22755	0.098000	0.18820	2.795000	0.47861	-0.130000	0.11599	-1.794000	0.00625	ACA		0	0.468										
SAGE2P	644717	bcgsc.ca	37	X	134807372	134807372	+	IGR	SNP	A	A	G	rs7890081		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:134807372A>G								DDX26B (90938 upstream) : CT45A1 (39812 downstream)																							GCACCTTCTCAAGTTGCTGAA	0.358													.|||	519	0.137483	0.1233	0.1124	3775	,	,		12470	0.126		0.0696	False		,,,				2504	0.0828				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTCTCAAGTTGC																													X.37:g.134807372A>G			134	0	0		172	0.15	26	.	0		0		RNA	SNP		37																																																																																					0	0.358										
SAGE2P	644717	bcgsc.ca	37	X	134814932	134814932	+	IGR	SNP	G	G	T	rs111943338		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:134814932G>T								DDX26B (98498 upstream) : CT45A1 (32252 downstream)																							TCTCTGGAACGTTTCTGTTTG	0.418													.|||	256	0.0678146	0.0416	0.0937	3775	,	,		17058	0.0466		0.0646	False		,,,				2504	0.0245				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGAACGTTTCTG																													X.37:g.134814932G>T			194	0.0051546392	1		218	0.12	27	.	0		0		RNA	SNP		37																																																																																					0	0.418										
Unknown	0	bcgsc.ca	37	X	141260813	141260813	+	IGR	SNP	G	G	T	rs1883360	byFrequency	TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:141260813G>T								MAGEC1 (263639 upstream) : MAGEC2 (29317 downstream)																							CTATTGTATAGCTTGGCCAAA	0.468													.|||	1226	0.324768	0.447	0.1787	3775	,	,		14679	0.1498		0.162	False		,,,				2504	0.2014				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTATAGCTTGGC																													X.37:g.141260813G>T			45	0	0		39	0.18	7	.	0		0		RNA	SNP		37																																																																																					0	0.468										
Unknown	0	bcgsc.ca	37	X	147279972	147279972	+	IGR	SNP	T	T	C	rs142596624		TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrX:147279972T>C								FMR1NB (171785 upstream) : AC002368.4 (299660 downstream)																							ACTATCTGGATACTTAAGCAT	0.532													T|||	182	0.0482119	0.0507	0.0389	3775	,	,		9506	0.002		0.0765	False		,,,				2504	0.0092				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGGATACTTAA																													X.37:g.147279972T>C			53	0	0		41	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.532										
MXRA5Y	286544	bcgsc.ca	37	Y	14107272	14107272	+	IGR	SNP	C	C	T			TCGA-W4-A7U3-01A-12D-A435-10	TCGA-W4-A7U3-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	6da5c14a-faa6-4741-a887-cc88c5d75ce2	c18a12ea-c02c-4166-8df1-b83a210c7dfb	g.chrY:14107272C>T								AC011293.1 (159760 upstream) : RN7SL702P (286904 downstream)																							ACGGCCATGGCGGGCCACACC	0.632																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	286544	.			CCATGGCGGGCCA																													Y.37:g.14107272C>T			108	0	0		67	0.24	16	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.632										
