#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_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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	ucsc.edu	37	1	1855319	1855319	+	IGR	SNP	C	C	T	rs2295362	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	115	0.0260869565	3		WXS	Illumina HiSeq		116	0.12	14	.	0		0		Missense_Mutation	SNP		37																																																																																					0	0.597										
CFAP74	85452	bcgsc.ca	37	1	1859176	1859176	+	IGR	SNP	T	T	C	rs45489198	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:1859176T>C								TMEM52 (8464 upstream) : C1orf222 (60386 downstream)																							GGGGCCATATTCTTTCGGAAC	0.617													C|||	1211	0.241813	0.5038	0.1124	5008	,	,		16151	0.1587		0.0437	False		,,,				2504	0.2689				.													.	.			0			.																																									SO:0001628	intergenic_variant	339457	.			CCATATTCTTTCG																													1.37:g.1859176T>C			Somatic	57	0	0		WXS	Illumina HiSeq	Phase_1	39	0.13	5	.	0		0		Missense_Mutation	SNP		37		381	0.17445054945054944	233	0.4735772357723577	39	0.10773480662983426	75	0.13111888111888112	34	0.044854881266490766	C	7.951	0.744957	0.15710	.	.	ENSG00000142609	ENST00000493964	T	0.20881	2.04	2.7	2.7	0.31948	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.099999999995774E-5	.	.	.	.	.	.	T	0.44498	-0.9324	5	0.12103	T	0.63	.	5.7933	0.18373	0.0:0.8485:0.0:0.1515	rs45489198;rs58102690	.	.	.	D	416	ENSP00000417061:N416D	ENSP00000417061:N416D	N	-	1	0	C1orf222	1849036	0.024000	0.19004	0.075000	0.20258	0.009000	0.06853	0.745000	0.26259	0.715000	0.32103	-0.695000	0.03696	AAT		0	0.617										
C1orf167	284498	bcgsc.ca	37	1	11835556	11835556	+	Missense_Mutation	SNP	C	C	T	rs41275456	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:11835556C>T	ENST00000433342.1	+	9	2125	c.2125C>T	c.(2125-2127)Cgc>Tgc	p.R709C	RP11-56N19.5_ENST00000376620.3_RNA|C1orf167_ENST00000484153.1_3'UTR			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		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_1	137	0.06	8	.	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	bcgsc.ca	37	1	11836628	11836628	+	Missense_Mutation	SNP	T	T	C	rs6699881	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:11836628T>C	ENST00000433342.1	+	10	2344	c.2344T>C	c.(2344-2346)Tgg>Cgg	p.W782R	RP11-56N19.5_ENST00000376620.3_RNA|C1orf167_ENST00000484153.1_3'UTR			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	782			W -> R (in dbSNP:rs6699881). {ECO:0000269|PubMed:17974005}.							central_nervous_system(1)	1						GGATGCCTGCTGGACACTGGC	0.682													C|||	3506	0.70008	0.5174	0.817	5008	,	,		16001	0.8839		0.7286	False		,,,				2504	0.6452				.													.	.			0			.																																									SO:0001583	missense	284498	.			GCCTGCTGGACAC	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.2344T>C	1.37:g.11836628T>C	ENSP00000414909:p.Trp782Arg		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_1	104	0.05	5	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		1618|1618	0.7408424908424909|0.7408424908424909	265|265	0.5386178861788617|0.5386178861788617	286|286	0.7900552486187845|0.7900552486187845	515|515	0.9003496503496503|0.9003496503496503	552|552	0.7282321899736148|0.7282321899736148	C|C	0.016|0.016	-1.528460|-1.528460	0.00959|0.00959	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000312793|ENST00000433342	.|T	.|0.04502	.|3.61	4.51|4.51	1.56|1.56	0.23342|0.23342	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.22034|0.22034	-1.0228|-1.0228	3|7	.|0.06365	.|T	.|0.9	-2.7535|-2.7535	4.8983|4.8983	0.13762|0.13762	0.0:0.4712:0.3374:0.1914|0.0:0.4712:0.3374:0.1914	rs6699881;rs6699881|rs6699881;rs6699881	.|782	.|Q5SNV9	.|CA167_HUMAN	P|R	141|782	.|ENSP00000414909:W782R	.|ENSP00000414909:W782R	L|W	+|+	2|1	0|0	C1orf167|C1orf167	11759215|11759215	0.007000|0.007000	0.16637|0.16637	0.015000|0.015000	0.15790|0.15790	0.036000|0.036000	0.12997|0.12997	-0.257000|-0.257000	0.08745|0.08745	-0.067000|-0.067000	0.12976|0.12976	-1.207000|-1.207000	0.01640|0.01640	CTG|TGG			0.682	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca;mdanderson.org	37	1	11836670	11836670	+	Silent	SNP	C	C	A	rs41275458	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:11836670C>A	ENST00000433342.1	+	10	2386	c.2386C>A	c.(2386-2388)Cgg>Agg	p.R796R	RP11-56N19.5_ENST00000376620.3_RNA|C1orf167_ENST00000484153.1_3'UTR			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			Somatic	248	0	0		WXS	Illumina HiSeq	Phase_1	172	0.10	17	.	0		0	Q8NDA9|Q8NDF3	Silent	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	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11838762	11838762	+	Silent	SNP	G	G	A	rs72640211	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	189	0	0		WXS	Illumina HiSeq		138	0.09	13	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_1	227	0.07	15	.	1	0.00	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	37	1	11839009	11839009	+	Silent	SNP	C	C	T	rs55685198	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	201	0	0		WXS	Illumina HiSeq	Phase_1	139	0.05	7	.	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					
Unknown	0	bcgsc.ca	37	1	12898045	12898045	+	IGR	SNP	G	G	A	rs10158988	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	108	0	0		WXS	Illumina HiSeq	Phase_1	72	0.21	15	.	0		0		RNA	SNP		37																																																																																					0	0.552										
Unknown	0	bcgsc.ca	37	1	12898378	12898378	+	IGR	SNP	C	C	G	rs57957396	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:12898378C>G								PRAMEF11 (7114 upstream) : HNRNPCL1 (8882 downstream)																							CAGCTCAGCCCTAATTGGGGT	0.493													.|||	939	0.1875	0.0197	0.2565	5008	,	,		15559	0.2748		0.2455	False		,,,				2504	0.2157				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCAGCCCTAATTG																													1.37:g.12898378C>G			Somatic	233	0	0		WXS	Illumina HiSeq	Phase_1	167	0.06	10	.	0		0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	1	12898445	12898445	+	IGR	SNP	C	C	A	rs11121996	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:12898445C>A								PRAMEF11 (7181 upstream) : HNRNPCL1 (8815 downstream)																							GGGGCAGGATCCATGTCCAGG	0.547													.|||	3678	0.734425	0.5318	0.866	5008	,	,		14840	0.6984		0.833	False		,,,				2504	0.8507				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGGATCCATGTC																													1.37:g.12898445C>A			Somatic	276	0	0		WXS	Illumina HiSeq	Phase_1	184	0.11	20	.	0		0		RNA	SNP		37																																																																																					0	0.547										
PRAMEF7	441871	bcgsc.ca;mdanderson.org	37	1	12980150	12980150	+	Missense_Mutation	SNP	A	A	G	rs113065075	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	366	0	0		WXS	Illumina HiSeq	Phase_1	318	0.08	24	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	
Unknown	0	bcgsc.ca	37	1	13183615	13183615	+	IGR	SNP	T	T	C	rs200176197		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:13183615T>C								RP13-221M14.3 (19147 upstream) : PRAMEF26 (32740 downstream)																							CTTTTGGCTCTGCAGCCAGGT	0.493																																					p.A86A													.	.			0			c.A258G												62.0	49.0	53.0					1																	13183615		692	1591	2283	SO:0001628	intergenic_variant	0	exon2			TGGCTCTGCAGCC																													1.37:g.13183615T>C			Somatic	201	0.0447761194	9		WXS	Illumina HiSeq	Phase_1	174	0.09	16	NM_001136561	1	0.00	0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	1	45457681	45457681	+	IGR	SNP	G	G	A	rs12126314	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:45457681G>A								EIF2B3 (5399 upstream) : HECTD3 (10530 downstream)																							CTTTGTTCGCGGAACAGGTAA	0.423													G|||	1617	0.322883	0.5015	0.4323	5008	,	,		22456	0.2748		0.1988	False		,,,				2504	0.181				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCGCGGAACAG																													1.37:g.45457681G>A			Somatic	54	0	0		WXS	Illumina HiSeq	Phase_1	57	0.07	4	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.423										
PSAT1P3	729779	bcgsc.ca	37	1	79520923	79520923	+	IGR	SNP	T	T	C	rs17131734	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:79520923T>C								ELTD1 (48520 upstream) : AC093430.1 (79894 downstream)																							ATTTGAGATTTGATGGAGCTA	0.433													T|||	969	0.19349	0.1369	0.2522	5008	,	,		20467	0.1548		0.174	False		,,,				2504	0.2883				.													.	.			0			.																																									SO:0001628	intergenic_variant	729779	.			GAGATTTGATGGA																													1.37:g.79520923T>C			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	36	0.17	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.433										
LOC100129138	100129138	bcgsc.ca	37	1	104615959	104615959	+	lincRNA	SNP	A	A	G	rs3811506	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	111	0	0		WXS	Illumina HiSeq	Phase_1	105	0.12	13	.	7	0.00	0		RNA	SNP	ENST00000418362.1	37																																																																																						0.552	RP11-364B6.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000030377.1			
NRBF2P3	643232	bcgsc.ca	37	1	111391513	111391513	+	IGR	SNP	C	C	T	rs12750061	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:111391513C>T								Y_RNA (84385 upstream) : CD53 (24261 downstream)																							ATGGTCTGCTCGTCTGCTCTG	0.498													c|||	1044	0.208466	0.1059	0.2968	5008	,	,		17426	0.1181		0.2843	False		,,,				2504	0.2996				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGCTCGTCTGC																													1.37:g.111391513C>T			Somatic	35	0	0		WXS	Illumina HiSeq	Phase_1	24	0.17	4	.	0		0		RNA	SNP		37																																																																																					0	0.498										
CNOT7P2	100132332	bcgsc.ca	37	1	116107337	116107337	+	IGR	SNP	T	T	A	rs41441746	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	58	0	0		WXS	Illumina HiSeq	Phase_1	51	0.10	5	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.398										
LOC728989	728989	bcgsc.ca	37	1	146522606	146522606	+	IGR	SNP	T	T	C	rs521687	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	168	0.005952381	1		WXS	Illumina HiSeq	Phase_1	158	0.14	22	.	8	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	93	0.0107526882	1		WXS	Illumina HiSeq	Phase_1	109	0.17	18	.	27	0.00	0		RNA	SNP		37																																																																																					0	0.418										
LOC728989	728989	bcgsc.ca	37	1	146523670	146523670	+	IGR	SNP	T	T	C	rs594716	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	45	0	0		WXS	Illumina HiSeq	Phase_1	61	0.15	9	.	0		0		RNA	SNP		37																																																																																					0	0.532										
Unknown	0	bcgsc.ca	37	1	147313509	147313509	+	IGR	SNP	C	C	T	rs146788179	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	153	0	0		WXS	Illumina HiSeq	Phase_1	156	0.07	11	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	226	0	0		WXS	Illumina HiSeq	Phase_1	261	0.07	17	.	110	0.00	0		RNA	SNP		37																																																																																					0	0.672										
Unknown	0	bcgsc.ca	37	1	157029199	157029199	+	IGR	SNP	A	A	G	rs11264607	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:157029199A>G								ARHGEF11 (14037 upstream) : ETV3L (32636 downstream)																							CAGTAGATCCATTCACCACGG	0.488													A|||	764	0.152556	0.0287	0.1556	5008	,	,		19476	0.2798		0.174	False		,,,				2504	0.1646				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGATCCATTCACC																													1.37:g.157029199A>G			Somatic	119	0	0		WXS	Illumina HiSeq	Phase_1	146	0.12	17	.	41	0.00	0		RNA	SNP		37																																																																																					0	0.488										
EI24P2	100129866	bcgsc.ca	37	1	158424637	158424637	+	IGR	SNP	A	A	C	rs1844787	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158424637A>C								OR10K2 (33981 upstream) : OR10K1 (10634 downstream)																							TCCATCTTGTAGGTCAGCTGG	0.428													C|||	4488	0.896166	0.9622	0.7954	5008	,	,		22586	0.8829		0.9195	False		,,,				2504	0.8681				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTTGTAGGTCAG																													1.37:g.158424637A>C			Somatic	82	0	0		WXS	Illumina HiSeq	Phase_1	60	0.18	11	.	0		0		RNA	SNP		37																																																																																					0	0.428										
Unknown	0	bcgsc.ca	37	1	158493554	158493554	+	IGR	SNP	A	A	G	rs6656837	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158493554A>G								RP11-144L1.4 (28878 upstream) : OR6Y1 (23363 downstream)																							AGTTGATGTCACTGATCATCA	0.413													A|||	317	0.0632987	0.1006	0.062	5008	,	,		16870	0.0		0.0984	False		,,,				2504	0.0429				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GATGTCACTGATC																													1.37:g.158493554A>G			Somatic	60	0	0		WXS	Illumina HiSeq	Phase_1	49	0.08	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.413										
Unknown	0	bcgsc.ca	37	1	158493726	158493726	+	IGR	SNP	C	C	T	rs7548349	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158493726C>T								RP11-144L1.4 (29050 upstream) : OR6Y1 (23191 downstream)																							AAATCAAACCCTCACTATTGT	0.398													C|||	2838	0.566693	0.6838	0.4683	5008	,	,		19365	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAAACCCTCACTA																													1.37:g.158493726C>T			Somatic	41	0	0		WXS	Illumina HiSeq	Phase_1	36	0.19	7	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	1	158493852	158493852	+	IGR	SNP	A	A	T	rs7514968	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158493852A>T								RP11-144L1.4 (29176 upstream) : OR6Y1 (23065 downstream)																							TATCTCTATGATTGGCCATTT	0.433													A|||	2838	0.566693	0.6838	0.4683	5008	,	,		19908	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTATGATTGGCC																													1.37:g.158493852A>T			Somatic	70	0	0		WXS	Illumina HiSeq	Phase_1	73	0.14	10	.	0		0		RNA	SNP		37																																																																																					0	0.433										
Unknown	0	bcgsc.ca	37	1	158493890	158493890	+	IGR	SNP	G	G	C	rs7525362	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158493890G>C								RP11-144L1.4 (29214 upstream) : OR6Y1 (23027 downstream)																							CTGCTTATTTGGTTGCCAAGA	0.458													G|||	2838	0.566693	0.6838	0.4683	5008	,	,		18975	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTATTTGGTTGCC																													1.37:g.158493890G>C			Somatic	61	0	0		WXS	Illumina HiSeq	Phase_1	67	0.12	8	.	0		0		RNA	SNP		37																																																																																					0	0.458										
Unknown	0	bcgsc.ca	37	1	158494110	158494110	+	IGR	SNP	A	A	G	rs7515245	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158494110A>G								RP11-144L1.4 (29434 upstream) : OR6Y1 (22807 downstream)																							TGGATATCCCATTACTCTTTT	0.333													G|||	2838	0.566693	0.6838	0.4683	5008	,	,		21071	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TATCCCATTACTC																													1.37:g.158494110A>G			Somatic	51	0	0		WXS	Illumina HiSeq	Phase_1	44	0.11	5	.	36	0.03	1		RNA	SNP		37																																																																																					0	0.333										
Unknown	0	bcgsc.ca	37	1	158494693	158494693	+	IGR	SNP	A	A	G	rs12145401	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158494693A>G								RP11-144L1.4 (30017 upstream) : OR6Y1 (22224 downstream)																							TTATCAGGAAAAATTTGGTCA	0.363													G|||	2838	0.566693	0.6838	0.4683	5008	,	,		19540	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGGAAAAATTTG																													1.37:g.158494693A>G			Somatic	41	0	0		WXS	Illumina HiSeq	Phase_1	68	0.19	13	.	0		0		RNA	SNP		37																																																																																					0	0.363										
Unknown	0	bcgsc.ca	37	1	158495209	158495209	+	IGR	SNP	C	C	T	rs6699473	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158495209C>T								RP11-144L1.4 (30533 upstream) : OR6Y1 (21708 downstream)																							GGTGGTTGTGCCAAACTGATT	0.363													T|||	2839	0.566893	0.6846	0.4683	5008	,	,		22797	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTGTGCCAAACT																													1.37:g.158495209C>T			Somatic	62	0	0		WXS	Illumina HiSeq	Phase_1	69	0.14	10	.	29	1.00	29		RNA	SNP		37																																																																																					0	0.363										
Unknown	0	bcgsc.ca	37	1	158495431	158495431	+	IGR	SNP	G	G	A	rs6674656	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158495431G>A								RP11-144L1.4 (30755 upstream) : OR6Y1 (21486 downstream)																							GGATCTGGTCGTCTTGCTTTA	0.458													A|||	2838	0.566693	0.6838	0.4683	5008	,	,		19758	0.5744		0.5755	False		,,,				2504	0.4611				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGGTCGTCTTGC																													1.37:g.158495431G>A			Somatic	59	0	0		WXS	Illumina HiSeq	Phase_1	57	0.11	6	.	0		0		RNA	SNP		37																																																																																					0	0.458										
OR10X1	128367	bcgsc.ca	37	1	158549420	158549421	+	Missense_Mutation	DNP	CG	CG	TA	rs863361|rs77690058	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:158549420_158549421CG>TA	ENST00000368150.1	-	1	268_269	c.269_270CG>TA	c.(268-270)aCG>aTA	p.T90I		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					CGATGGTCAGCGTATAGCAGGT	0.495																																					p.T90I													OR10X1,face,carcinoma,-1,1	OR10X1	96	1	0			c.C269T																																									SO:0001583	missense	128367	exon1			GGTCAGCGTATAG	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.269_270delinsTA	1.37:g.158549420_158549421delinsTA	ENSP00000357132:p.Thr90Ile		Somatic	126	0.0079365079	1		WXS	Illumina HiSeq	Phase_1	151	0.05	7	NM_001004477	0		0	Q6IFR8	Missense_Mutation	DNP	ENST00000368150.1	37	CCDS30900.1																																																																																					0.495	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000051850.2		NM_001004477	
UAP1	6675	ucsc.edu	37	1	162549362	162549362	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:162549362G>T	ENST00000367925.1	+	3	662	c.630G>T	c.(628-630)ttG>ttT	p.L210F	UAP1_ENST00000367924.1_Missense_Mutation_p.L210F|UAP1_ENST00000271469.3_Missense_Mutation_p.L210F|UAP1_ENST00000367926.4_Missense_Mutation_p.L210F			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	210					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|UDP-N-acetylglucosamine diphosphorylase activity (GO:0003977)			breast(2)|cervix(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)|skin(2)|stomach(1)	22	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			AAATTATTTTGGAAGAGAAGA	0.338																																					p.L210F													.	UAP1	47		0			c.G630T												70.0	73.0	72.0					1																	162549362		2200	4299	6499	SO:0001583	missense	6675	exon4			TATTTTGGAAGAG	AB011004	CCDS1240.1	1q23.2	2014-07-31	2014-07-31		ENSG00000117143	ENSG00000117143	2.7.7.23		12457	protein-coding gene	gene with protein product		602862		SPAG2		9603950, 8025165	Standard	NM_003115		Approved	AGX1, AgX	uc001gce.4	Q16222	OTTHUMG00000034419	ENST00000367925.1:c.630G>T	1.37:g.162549362G>T	ENSP00000356902:p.Leu210Phe		Somatic	51	0	0		WXS	Illumina HiSeq		43	0.09	4	NM_003115	98	0.00	0	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Missense_Mutation	SNP	ENST00000367925.1	37		.	.	.	.	.	.	.	.	.	.	G	19.49	3.837886	0.71373	.	.	ENSG00000117143	ENST00000412525;ENST00000367926;ENST00000271469;ENST00000367925;ENST00000367924	T;T;T;T;T	0.22539	1.95;1.95;1.95;1.95;1.95	5.38	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.31358	0.0794	M	0.83384	2.64	0.58432	D	0.999995	D	0.89917	1.0	D	0.81914	0.995	T	0.24799	-1.0150	9	0.87932	D	0	-15.2827	8.7399	0.34552	0.3742:0.0:0.6258:0.0	.	210	Q16222-2	.	F	210	ENSP00000395648:L210F;ENSP00000356903:L210F;ENSP00000271469:L210F;ENSP00000356902:L210F;ENSP00000356901:L210F	ENSP00000271469:L210F	L	+	3	2	UAP1	160815986	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	1.520000	0.35899	0.008000	0.14787	0.655000	0.94253	TTG			0.338	UAP1-002	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000083203.1		NM_003115	
TMEM78	677790	broad.mit.edu;bcgsc.ca	37	1	229385670	229385671	+	Frame_Shift_Del	DEL	TC	TC	-	rs71561726|rs140311590|rs35330340	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TC	TC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:229385670_229385671delTC	ENST00000323223.2	+	1	288_289	c.229_230delTC	c.(229-231)tctfs	p.S77fs				Q5T7P6	TMM78_HUMAN	transmembrane protein 78	77						integral component of membrane (GO:0016021)											tctctctctttctctctttctt	0.465														787	0.157149	0.2648	0.0937	5008	,	,		19793	0.0833		0.1431	False		,,,				2504	0.1472				.													.	.			0			.																																									SO:0001589	frameshift_variant	677790	.			TCTCTTTCTCTCT	AK097487		1q42.13	2008-08-27			ENSG00000177800	ENSG00000177800			32307	protein-coding gene	gene with protein product							Standard			Approved	FLJ40168		Q5T7P6	OTTHUMG00000037629	ENST00000323223.2:c.229_230delTC	1.37:g.229385674_229385675delTC	ENSP00000324799:p.Ser77fs		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	12	0.50	6	.	0		0	Q8N802	Frame_Shift_Del	DEL	ENST00000323223.2	37																																																																																						0.465	TMEM78-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000091730.2			
Unknown	0	bcgsc.ca	37	1	236274147	236274147	+	IGR	SNP	G	G	A	rs7516388	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:236274147G>A								NID1 (45685 upstream) : GPR137B (31684 downstream)																							CAGGCCTGGCGTAGACTCCAT	0.552													g|||	2065	0.41234	0.4047	0.4914	5008	,	,		19472	0.4395		0.3936	False		,,,				2504	0.3579				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTGGCGTAGACT																													1.37:g.236274147G>A			Somatic	38	0	0		WXS	Illumina HiSeq	Phase_1	42	0.12	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.552										
Unknown	0	bcgsc.ca	37	1	240136252	240136252	+	IGR	SNP	C	C	T	rs72762530	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:240136252C>T								RP11-35L17.3 (55997 upstream) : FMN2 (118927 downstream)																							TTGCACTGGCCGACTGGAAGT	0.438													C|||	204	0.0407348	0.0182	0.049	5008	,	,		20259	0.001		0.0984	False		,,,				2504	0.047				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACTGGCCGACTGG																													1.37:g.240136252C>T			Somatic	34	0	0		WXS	Illumina HiSeq	Phase_1	50	0.12	6	.	0		0		RNA	SNP		37																																																																																					0	0.438										
OR14A2	388761	bcgsc.ca;mdanderson.org	37	1	247886493	247886493	+	Missense_Mutation	SNP	G	G	A	rs62619787	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:247886493G>A	ENST00000366485.1	-	1	852	c.853C>T	c.(853-855)Cct>Tct	p.P285S	RP11-634B7.5_ENST00000426444.1_RNA|RP11-634B7.4_ENST00000449298.1_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		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_1	171	0.07	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	37	1	247886949	247886949	+	Missense_Mutation	SNP	T	T	C	rs36075193	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:247886949T>C	ENST00000366485.1	-	1	396	c.397A>G	c.(397-399)Atc>Gtc	p.I133V	RP11-634B7.5_ENST00000426444.1_RNA|RP11-634B7.4_ENST00000449298.1_RNA			Q96R54	O14A2_HUMAN	olfactory receptor, family 14, subfamily A, member 2	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										GTATTCATGATTACCTCGTAG	0.468													T|||	189	0.0377396	0.0053	0.0476	5008	,	,		21772	0.001		0.1272	False		,,,				2504	0.0204				.													.	.			0			.																																									SO:0001583	missense	388761	.			TCATGATTACCTC	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.397A>G	1.37:g.247886949T>C	ENSP00000355441:p.Ile133Val		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_1	122	0.07	8	.	0		0		Missense_Mutation	SNP	ENST00000366485.1	37		111	0.050824175824175824	4	0.008130081300813009	21	0.058011049723756904	1	0.0017482517482517483	85	0.11213720316622691	T	1.446	-0.566297	0.03910	.	.	ENSG00000241128	ENST00000366485	T	0.19669	2.13	3.18	0.633	0.17712	.	0.314707	0.23017	N	0.052889	T	0.00271	0.0008	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.24476	-1.0159	7	0.27785	T	0.31	.	5.1576	0.15044	0.1374:0.1898:0.0:0.6729	rs36075193	.	.	.	V	133	ENSP00000355441:I133V	ENSP00000355441:I133V	I	-	1	0	OR14A2	245953572	0.000000	0.05858	0.027000	0.17364	0.150000	0.21749	-0.517000	0.06275	-0.322000	0.08615	-1.139000	0.01908	ATC			0.468	OR14A2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000096864.1		NG_002409	
HSD17B7P1	148818	bcgsc.ca	37	1	247991516	247991516	+	IGR	SNP	C	C	G	rs6698863	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr1:247991516C>G								OR14A16 (12485 upstream) : OR11L1 (12682 downstream)																							GTTGATGCCACTAATATGGCT	0.423													C|||	661	0.131989	0.3487	0.0807	5008	,	,		22127	0.0149		0.0388	False		,,,				2504	0.092				.													.	.			0			.																																									SO:0001628	intergenic_variant	148818	.			ATGCCACTAATAT																													1.37:g.247991516C>G			Somatic	72	0	0		WXS	Illumina HiSeq	Phase_1	58	0.09	5	.	0		0		RNA	SNP		37																																																																																					0	0.423										
PRPF38AP1	389935	bcgsc.ca	37	10	8203302	8203302	+	IGR	SNP	T	T	C	rs2664906	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:8203302T>C								GATA3 (86141 upstream) : LINC00708 (97991 downstream)																							ATCATTCGAATGCGAATCTGT	0.488													C|||	3018	0.602636	0.5772	0.6167	5008	,	,		14062	0.5179		0.6889	False		,,,				2504	0.6258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCGAATGCGAAT																													10.37:g.8203302T>C			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	40	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.488										
MYO3A	53904	ucsc.edu;bcgsc.ca	37	10	26357747	26357748	+	Missense_Mutation	DNP	CG	CG	TA	rs35379457|rs3817420|rs386742102	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:26357747_26357748CG>TA	ENST00000265944.5	+	12	1270_1271	c.1104_1105CG>TA	c.(1102-1107)taCGtc>taTAtc	p.V369I	MYO3A_ENST00000543632.1_Missense_Mutation_p.V369I	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	369	Myosin motor.		V -> I (in dbSNP:rs3817420). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATCAGATCTACGTCTATGTGGG	0.371																																					p.V369I													.	MYO3A	371		0			c.G1105A																																									SO:0001583	missense	53904	exon12			GATCTACGTCTAT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	Exception_encountered	10.37:g.26357747_26357748delinsTA	ENSP00000265944:p.Val369Ile		Somatic	84	0	0		WXS	Illumina HiSeq		86	0.10	9	NM_017433	6	0.00	0	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	DNP	ENST00000265944.5	37	CCDS7148.1																																																																																					0.371	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000047259.1		NM_017433	
ARL6IP1P2	646348	bcgsc.ca	37	10	37284272	37284272	+	IGR	SNP	A	A	G	rs10764117	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:37284272A>G								RP11-322I2.1 (51412 upstream) : ANKRD30A (130512 downstream)																							CTGTGGGTTGATGGAAACGCC	0.438													G|||	3439	0.686701	0.5567	0.6513	5008	,	,		19967	0.7946		0.675	False		,,,				2504	0.7883				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGTTGATGGAAA																													10.37:g.37284272A>G			Somatic	61	0	0		WXS	Illumina HiSeq	Phase_1	50	0.18	9	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.438										
ASAH2C	653365	bcgsc.ca;mdanderson.org	37	10	48003992	48003992	+	Missense_Mutation	SNP	C	C	T	rs142685947|rs3739968	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	1430	0.0013986014	2		WXS	Illumina HiSeq	Phase_1	936	0.06	57	.	12	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	
Unknown	0	bcgsc.ca;mdanderson.org	37	10	49313245	49313245	+	IGR	SNP	C	C	T	rs2270911	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:49313245C>T								RNA5SP315 (64654 upstream) : RP11-13E1.5 (50122 downstream)																							GCAGCCTCCTCATCCTCACTG	0.488													C|||	2256	0.450479	0.5363	0.3285	5008	,	,		10884	0.7073		0.341	False		,,,				2504	0.2689				.													PTPN20C_ENST00000455582,bladder,carcinoma,0,9	.		9	0			.																																									SO:0001628	intergenic_variant	653045	.			CCTCCTCATCCTC																													10.37:g.49313245C>T			Somatic	347	0	0		WXS	Illumina HiSeq	Phase_1	264	0.10	27	.	0		0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	12.58	1.980355	0.34942	.	.	ENSG00000126542	ENST00000316733;ENST00000455582	.	.	.	2.99	-0.298	0.12814	.	.	.	.	.	T	0.22282	0.0537	.	.	.	.	.	.	.	.	.	.	.	.	T	0.35773	-0.9775	4	0.13108	T	0.6	.	5.2137	0.15331	0.41:0.3891:0.2008:0.0	rs2270911;rs2270911	.	.	.	K	96;99	.	ENSP00000313973:E96K	E	-	1	0	PTPN20C	48983251	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	0.191000	0.17076	-0.051000	0.13334	0.194000	0.17425	GAG		0	0.488										
NUTM2HP	729023	bcgsc.ca	37	10	52443585	52443585	+	IGR	SNP	T	T	C	rs11006622	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:52443585T>C								RP11-564C4.6 (23557 upstream) : ASAH2B (55492 downstream)																							GAGGACTGGATGCCCCCAGAC	0.617													N|||	191	0.038139	0.0983	0.0303	5008	,	,		16165	0.0119		0.0139	False		,,,				2504	0.0143				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACTGGATGCCCCC																													10.37:g.52443585T>C			Somatic	179	0	0		WXS	Illumina HiSeq	Phase_1	144	0.06	9	.	0		0		RNA	SNP		37																																																																																					0	0.617										
AKR1B10P1	340888	bcgsc.ca	37	10	69510905	69510905	+	IGR	SNP	C	C	T	rs10997795	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:69510905C>T								CTNNA3 (54978 upstream) : DNAJC12 (45521 downstream)																							ATGGCAACCACACTCAGCTTC	0.468													T|||	1360	0.271565	0.3767	0.1614	5008	,	,		20962	0.4345		0.0885	False		,,,				2504	0.228				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAACCACACTCAG																													10.37:g.69510905C>T			Somatic	64	0	0		WXS	Illumina HiSeq	Phase_1	40	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.468										
ZSWIM8	23053	bcgsc.ca	37	10	75551642	75551642	+	Missense_Mutation	SNP	C	C	T	rs201390871	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr10:75551642C>T	ENST00000605216.1	+	10	1562	c.1345C>T	c.(1345-1347)Cgg>Tgg	p.R449W	ZSWIM8_ENST00000604524.1_Missense_Mutation_p.R449W|ZSWIM8_ENST00000398706.2_Missense_Mutation_p.R449W|ZSWIM8_ENST00000603114.1_Missense_Mutation_p.R449W|ZSWIM8_ENST00000604729.1_Missense_Mutation_p.R449W	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	449							zinc ion binding (GO:0008270)										TACGCAGCTGCGGCAGTGGCA	0.632													C|||	6	0.00119808	0.0008	0.0058	5008	,	,		17125	0.0		0.001	False		,,,				2504	0.0				p.R449W													.	.			0			c.C1345T							C	TRP/ARG,TRP/ARG,TRP/ARG	0,3946		0,0,1973	10.0	13.0	12.0		1345,1345,1345	5.4	1.0	10		12	1,8145		0,1,4072	yes	missense,missense,missense	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	101,101,101	0,1,6045	TT,TC,CC		0.0123,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging	449/1838,449/1893,449/1843	75551642	1,12091	1973	4073	6046	SO:0001583	missense	23053	exon10			CAGCTGCGGCAGT	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.1345C>T	10.37:g.75551642C>T	ENSP00000474748:p.Arg449Trp		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_1	74	0.07	5	NM_015037	28	0.00	0	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Missense_Mutation	SNP	ENST00000605216.1	37		6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	C|C	16.94|16.94	3.261520|3.261520	0.59431|0.59431	0.0|0.0	1.23E-4|1.23E-4	ENSG00000214655|ENSG00000214655	ENST00000433366|ENST00000398706	.|T	.|0.73575	.|-0.76	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	.|0.111390	.|0.34314	.|U	.|0.004079	T|T	0.68247|0.68247	0.2980|0.2980	N|N	0.22421|0.22421	0.69|0.69	0.41976|0.41976	D|D	0.990776|0.990776	.|D;D;D	.|0.71674	.|0.998;0.998;0.998	.|P;P;P	.|0.59546	.|0.802;0.859;0.802	T|T	0.75545|0.75545	-0.3280|-0.3280	5|10	.|0.72032	.|D	.|0.01	-6.8518|-6.8518	13.9614|13.9614	0.64182|0.64182	0.1873:0.8127:0.0:0.0|0.1873:0.8127:0.0:0.0	.|.	.|449;449;449	.|A7E2V4;A7E2V4-5;A7E2V4-4	.|K0913_HUMAN;.;.	V|W	171|449	.|ENSP00000381693:R449W	.|ENSP00000381693:R449W	A|R	+|+	2|1	0|2	KIAA0913|KIAA0913	75221648|75221648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.827000|0.827000	0.46813|0.46813	3.333000|3.333000	0.52090|0.52090	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GCG|CGG			0.632	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000468545.1		NM_001242487	
SCGB1C1	147199	bcgsc.ca	37	11	194441	194441	+	Silent	SNP	C	C	T	rs61997072	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:194441C>T	ENST00000342878.2	+	3	299	c.279C>T	c.(277-279)gaC>gaT	p.D93D	ODF3_ENST00000325113.4_5'Flank|BET1L_ENST00000410108.1_Intron|ODF3_ENST00000342593.5_5'Flank|ODF3_ENST00000525282.1_5'Flank	NM_145651.2	NP_663626.2	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1	93						extracellular region (GO:0005576)				endometrium(1)|liver(2)|lung(1)|skin(1)	5		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCAGTCAGGACGGTGCCTAAG	0.567																																					p.D93D													.	.			0			c.C279T							C		367,3961		0,367,1797	152.0	159.0	156.0		279	-8.3	0.0	11	dbSNP_129	156	1062,7450		0,1062,3194	no	coding-synonymous	SCGB1C1	NM_145651.2		0,1429,4991	TT,TC,CC		12.4765,8.4797,11.1293		93/96	194441	1429,11411	2164	4256	6420	SO:0001819	synonymous_variant	147199	exon3			TCAGGACGGTGCC	AY026938	CCDS41581.1	11p15.5	2011-12-14			ENSG00000188076	ENSG00000188076		"""Secretoglobins"""	18394	protein-coding gene	gene with protein product		610176				22155607	Standard	NM_145651		Approved	RYD5	uc001loa.1	Q8TD33	OTTHUMG00000165539	ENST00000342878.2:c.279C>T	11.37:g.194441C>T			Somatic	124	0	0		WXS	Illumina HiSeq	Phase_1	86	0.07	6	NM_001097610	1	0.00	0	A8MSI9|Q14DW0	Silent	SNP	ENST00000342878.2	37	CCDS41581.1																																																																																					0.567	SCGB1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000384759.1		NM_145651	
FAM86GP	387745	bcgsc.ca	37	11	3437850	3437850	+	IGR	SNP	G	G	A			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:3437850G>A								TSSC2 (7642 upstream) : RP13-726E6.1 (52698 downstream)																							TTGTCCAAAAGCTCTGTGTGG	0.527																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	387745	.			CCAAAAGCTCTGT																													11.37:g.3437850G>A			Somatic	99	0	0		WXS	Illumina HiSeq	Phase_1	76	0.07	5	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.527										
FAM86GP	387745	bcgsc.ca	37	11	3439455	3439455	+	IGR	SNP	A	A	C	rs12421377	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:3439455A>C								TSSC2 (9247 upstream) : RP13-726E6.1 (51093 downstream)																							GAGAGAAAGCACCGGGCATAC	0.562													-|||	169	0.033746	0.0038	0.062	5008	,	,		19521	0.003		0.0736	False		,,,				2504	0.045				.													.	.			0			.																																									SO:0001628	intergenic_variant	387745	.			GAAAGCACCGGGC																													11.37:g.3439455A>C			Somatic	75	0	0		WXS	Illumina HiSeq	Phase_1	71	0.07	5	.	0		0		RNA	SNP		37																																																																																					0	0.562										
OTOG	340990	bcgsc.ca	37	11	17579783	17579783	+	Missense_Mutation	SNP	C	C	A	rs61611064	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:17579783C>A	ENST00000399391.2	+	8	953	c.953C>A	c.(952-954)gCc>gAc	p.A318D	OTOG_ENST00000399397.1_Missense_Mutation_p.A245D	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	318	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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						CAGGAGCAGGCCCCTAACCAG	0.622													C|||	567	0.113219	0.0431	0.1052	5008	,	,		18360	0.0565		0.1829	False		,,,				2504	0.2004				.													.	.			0			.																																									SO:0001583	missense	340990	.			AGCAGGCCCCTAA	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.953C>A	11.37:g.17579783C>A	ENSP00000382323:p.Ala318Asp		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_1	96	0.08	8	.	0		0	A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	ENST00000399391.2	37	CCDS59225.1	218	0.09981684981684982	27	0.054878048780487805	46	0.1270718232044199	26	0.045454545454545456	119	0.15699208443271767	C	13.20	2.165932	0.38217	.	.	ENSG00000188162	ENST00000399391;ENST00000399397	T;T	0.15139	2.45;2.55	5.66	1.71	0.24356	.	0.592366	0.14471	U	0.317594	T	0.00039	0.0001	N	0.16602	0.42	0.80722	P	0.0	.	.	.	.	.	.	T	0.37502	-0.9703	7	0.02654	T	1	.	4.3675	0.11232	0.1475:0.5306:0.0:0.3219	rs61611064;rs61744968	.	.	.	D	318;245	ENSP00000382323:A318D;ENSP00000382329:A245D	ENSP00000382323:A318D	A	+	2	0	OTOG	17536359	0.001000	0.12720	0.461000	0.27105	0.961000	0.63080	0.445000	0.21677	0.321000	0.23259	0.591000	0.81541	GCC			0.622	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
OTOG	340990	bcgsc.ca;mdanderson.org	37	11	17593709	17593709	+	Missense_Mutation	SNP	T	T	C	rs7106548|rs386751105	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:17593709T>C	ENST00000399391.2	+	17	2074	c.2074T>C	c.(2074-2076)Tct>Cct	p.S692P	OTOG_ENST00000399397.1_Missense_Mutation_p.S619P	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	692	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.		S -> P (in dbSNP:rs7106548).		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						CCCGCTGGTCTCTGGCTCCCC	0.592													C|||	2208	0.440895	0.6664	0.3242	5008	,	,		16926	0.3204		0.4155	False		,,,				2504	0.3691				.													.	.			0			.																																									SO:0001583	missense	340990	.			CTGGTCTCTGGCT	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.2074T>C	11.37:g.17593709T>C	ENSP00000382323:p.Ser692Pro		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_1	129	0.07	9	.	0		0	A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	ENST00000399391.2	37	CCDS59225.1	904	0.4139194139194139	327	0.6646341463414634	116	0.32044198895027626	144	0.2517482517482518	317	0.4182058047493404	C	8.490	0.861886	0.17178	.	.	ENSG00000188162	ENST00000399391;ENST00000399397	T;T	0.16196	2.36;2.47	5.4	-4.21	0.03812	.	1.182810	0.06452	N	0.727832	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	.	.	.	.	.	.	T	0.34204	-0.9838	7	0.25106	T	0.35	.	8.5735	0.33583	0.0:0.2638:0.2909:0.4453	rs7106548;rs52794588;rs60134828;rs7106548	.	.	.	P	692;619	ENSP00000382323:S692P;ENSP00000382329:S619P	ENSP00000382323:S692P	S	+	1	0	OTOG	17550285	0.000000	0.05858	0.003000	0.11579	0.641000	0.38312	0.032000	0.13732	-1.041000	0.03266	-0.213000	0.12676	TCT			0.592	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
OTOG	340990	bcgsc.ca;mdanderson.org	37	11	17596313	17596313	+	Silent	SNP	G	G	A	rs4757548	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:17596313G>A	ENST00000399391.2	+	19	2376	c.2376G>A	c.(2374-2376)ccG>ccA	p.P792P	OTOG_ENST00000399397.1_Silent_p.P719P	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	792	TIL.				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						GCGTGGCCCCGTGTGGACGTA	0.632													G|||	1672	0.333866	0.3759	0.2435	5008	,	,		20095	0.2986		0.3976	False		,,,				2504	0.3119				.													.	.			0			.																																									SO:0001819	synonymous_variant	340990	.			GGCCCCGTGTGGA	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.2376G>A	11.37:g.17596313G>A			Somatic	61	0	0		WXS	Illumina HiSeq	Phase_1	55	0.15	8	.	0		0	A8MTX6|A8MUJ0|B7WPC4	Silent	SNP	ENST00000399391.2	37	CCDS59225.1																																																																																					0.632	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
OTOG	340990	ucsc.edu;mdanderson.org	37	11	17600033	17600033	+	Missense_Mutation	SNP	G	G	A	rs2355466	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:17600033G>A	ENST00000399391.2	+	22	2755	c.2755G>A	c.(2755-2757)Gcc>Acc	p.A919T	OTOG_ENST00000342528.2_5'UTR|OTOG_ENST00000399397.1_Missense_Mutation_p.A846T	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	919			A -> T (in dbSNP:rs2355466).		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						GAGCGTGTCAGCCCGTGGCCC	0.647													G|||	1383	0.276158	0.1914	0.2133	5008	,	,		19813	0.2579		0.3946	False		,,,				2504	0.3323				.													.	.			0			.																																									SO:0001583	missense	340990	.			GTGTCAGCCCGTG	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.2755G>A	11.37:g.17600033G>A	ENSP00000382323:p.Ala919Thr		Somatic	17	0	0		WXS	Illumina HiSeq		21	0.29	6	.	0		0	A8MTX6|A8MUJ0|B7WPC4	Missense_Mutation	SNP	ENST00000399391.2	37	CCDS59225.1	604	0.2765567765567766	106	0.21544715447154472	83	0.2292817679558011	117	0.20454545454545456	298	0.39313984168865435	G	11.42	1.634111	0.29068	.	.	ENSG00000188162	ENST00000399391;ENST00000399397	T;T	0.29655	1.56;1.56	5.79	4.88	0.63580	.	0.221212	0.29172	U	0.012921	T	0.00012	0.0000	N	0.11560	0.145	0.30377	P	0.782309	.	.	.	.	.	.	T	0.45906	-0.9229	7	0.13108	T	0.6	.	13.1262	0.59356	0.0748:0.0:0.9252:0.0	rs2355466;rs17716033;rs52836272;rs2355466	.	.	.	T	919;846	ENSP00000382323:A919T;ENSP00000382329:A846T	ENSP00000382323:A919T	A	+	1	0	OTOG	17556609	0.993000	0.37304	0.936000	0.37596	0.634000	0.38068	2.394000	0.44450	1.471000	0.48121	-0.189000	0.12847	GCC			0.647	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
OTOG	340990	bcgsc.ca	37	11	17656686	17656686	+	Silent	SNP	C	C	T	rs11024350	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:17656686C>T	ENST00000399391.2	+	45	7681	c.7681C>T	c.(7681-7683)Ctg>Ttg	p.L2561L	OTOG_ENST00000342528.2_Intron|OTOG_ENST00000399397.1_Silent_p.L2488L	NM_001277269.1	NP_001264198.1	Q6ZRI0	OTOG_HUMAN	otogelin	2561	Cys-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						GGACCAGATCCTGATCACGGG	0.637													C|||	732	0.146166	0.0628	0.0778	5008	,	,		12859	0.244		0.1362	False		,,,				2504	0.2168				.													.	.			0			.																																									SO:0001819	synonymous_variant	340990	.			CAGATCCTGATCA	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.7681C>T	11.37:g.17656686C>T			Somatic	63	0	0		WXS	Illumina HiSeq	Phase_1	62	0.08	5	.	2	0.00	0	A8MTX6|A8MUJ0|B7WPC4	Silent	SNP	ENST00000399391.2	37	CCDS59225.1																																																																																					0.637	OTOG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding					
FIBP	9158	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	65651461	65651461	+	Missense_Mutation	SNP	C	C	T	rs140853801		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:65651461C>T	ENST00000338369.2	-	10	1191	c.1079G>A	c.(1078-1080)cGc>cAc	p.R360H	FIBP_ENST00000533045.1_Silent_p.A345A|FIBP_ENST00000357519.4_Missense_Mutation_p.R353H|FIBP_ENST00000426652.2_5'Flank	NM_198897.1	NP_942600.1	O43427	FIBP_HUMAN	fibroblast growth factor (acidic) intracellular binding protein	360					fibroblast growth factor receptor signaling pathway (GO:0008543)|platelet aggregation (GO:0070527)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	10				READ - Rectum adenocarcinoma(159;0.166)		ATGATACAGGCGCAGGAGGCA	0.592											OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R360H													FIBP,colon,carcinoma,0,1	FIBP	0	1	0			c.G1079A							C	HIS/ARG,HIS/ARG	3,4399	6.2+/-15.9	0,3,2198	67.0	61.0	63.0		1058,1079	3.9	1.0	11	dbSNP_134	63	1,8591	1.2+/-3.3	0,1,4295	yes	missense,missense	FIBP	NM_004214.4,NM_198897.1	29,29	0,4,6493	TT,TC,CC		0.0116,0.0682,0.0308	benign,benign	353/358,360/365	65651461	4,12990	2201	4296	6497	SO:0001583	missense	9158	exon10			TACAGGCGCAGGA	AF010187	CCDS8118.1, CCDS8119.1	11q13.1	2006-06-15			ENSG00000172500	ENSG00000172500			3705	protein-coding gene	gene with protein product		608296				9806903	Standard	NM_004214		Approved	FGFIBP	uc001ogd.3	O43427	OTTHUMG00000166846	ENST00000338369.2:c.1079G>A	11.37:g.65651461C>T	ENSP00000344572:p.Arg360His		Somatic	89	0	0	1085	WXS	Illumina HiSeq	.	75	0.13	10	NM_198897	219	0.19	42	A8K0J7|Q27Q85|Q6IBQ3|Q9HD65	Missense_Mutation	SNP	ENST00000338369.2	37	CCDS8119.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.433949	0.62955	6.82E-4	1.16E-4	ENSG00000172500	ENST00000338369;ENST00000357519	T;T	0.25250	1.81;1.81	4.83	3.9	0.45041	.	0.132036	0.50627	D	0.000117	T	0.22205	0.0535	L	0.36672	1.1	0.80722	D	1	D;D	0.54207	0.957;0.965	B;P	0.46389	0.294;0.515	T	0.01133	-1.1441	10	0.72032	D	0.01	-15.6946	6.7408	0.23435	0.0:0.8028:0.0:0.1972	.	353;360	O43427-2;O43427	.;FIBP_HUMAN	H	360;353	ENSP00000344572:R360H;ENSP00000350124:R353H	ENSP00000344572:R360H	R	-	2	0	FIBP	65408037	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.987000	0.49378	2.385000	0.81259	0.555000	0.69702	CGC	0		0.592	FIBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000391575.2		NM_198897	
PIWIL4	143689	bcgsc.ca	37	11	94322352	94322353	+	Missense_Mutation	DNP	AG	AG	TA	rs11020846|rs11020845|rs386756343	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:94322352_94322353AG>TA	ENST00000299001.6	+	8	1191_1192	c.980_981AG>TA	c.(979-981)cAG>cTA	p.Q327L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	327	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		Q -> L (in dbSNP:rs11020845). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CACACCTTTCAGAAGCGGGATG	0.396																																					p.Q327L													.	PIWIL4	70		0			c.G981A																																									SO:0001583	missense	143689	exon8			CCTTTCAGAAGCG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		Exception_encountered	11.37:g.94322352_94322353delinsTA	ENSP00000299001:p.Gln327Leu		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_1	47	0.11	5	NM_152431	15	0.00	0	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	DNP	ENST00000299001.6	37	CCDS31656.1																																																																																					0.396	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000396388.1		NM_152431	
GLULP3	401708	bcgsc.ca	37	11	122484722	122484722	+	IGR	SNP	C	C	T	rs61910452	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr11:122484722C>T								RNU6-592P (34707 upstream) : UBASH3B (41660 downstream)																							CTCCAGCTTACAAGCAGGCCC	0.537													C|||	1111	0.221845	0.0983	0.3242	5008	,	,		19735	0.1131		0.3022	False		,,,				2504	0.3456				.													.	.			0			.																																									SO:0001628	intergenic_variant	401708	.			AGCTTACAAGCAG																													11.37:g.122484722C>T			Somatic	111	0	0		WXS	Illumina HiSeq	Phase_1	54	0.19	10	.	0		0		RNA	SNP		37																																																																																					0	0.537										
SLC6A13	6540	ucsc.edu	37	12	351879	351879	+	Missense_Mutation	SNP	C	C	A			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:351879C>A	ENST00000343164.4	-	4	431	c.379G>T	c.(379-381)Gtc>Ttc	p.V127F	SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	127					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			ATGTAGTAGACGTTGAGGAGG	0.582																																					p.V127F													SLC6A13,caecum,carcinoma,0,2	SLC6A13	62	2	0			c.G379T												118.0	80.0	93.0					12																	351879		2203	4300	6503	SO:0001583	missense	6540	exon4			AGTAGACGTTGAG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.379G>T	12.37:g.351879C>A	ENSP00000339260:p.Val127Phe		Somatic	98	0.0204081633	2		WXS	Illumina HiSeq		159	0.14	22	NM_016615	0		0	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486750	0.44249	.	.	ENSG00000010379	ENST00000313154;ENST00000343164	T	0.75154	-0.91	5.61	-6.23	0.02052	.	0.723628	0.13885	N	0.356028	T	0.52403	0.1732	N	0.17082	0.46	0.80722	D	1	B;B	0.16396	0.017;0.005	B;B	0.33890	0.172;0.11	T	0.31110	-0.9955	10	0.10902	T	0.67	.	8.4922	0.33106	0.5385:0.3283:0.0:0.1332	.	106;127	B4DJS3;Q9NSD5	.;S6A13_HUMAN	F	106;127	ENSP00000339260:V127F	ENSP00000318097:V106F	V	-	1	0	SLC6A13	222140	0.507000	0.26146	0.809000	0.32408	0.981000	0.71138	-0.104000	0.10923	-1.613000	0.01577	-0.397000	0.06425	GTC			0.582	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000397801.1		NM_016615	
Unknown	0	bcgsc.ca	37	12	6588445	6588445	+	IGR	SNP	A	A	G	rs2008134	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	34	0	0		WXS	Illumina HiSeq	Phase_1	70	0.09	6	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.483										
PEX5	5830	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	7354887	7354887	+	Silent	SNP	C	C	T	rs140332077		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:7354887C>T	ENST00000455147.2	+	9	1273	c.693C>T	c.(691-693)tcC>tcT	p.S231S	PEX5_ENST00000434354.2_Silent_p.S246S|PEX5_ENST00000412720.2_Silent_p.S252S|PEX5_ENST00000266563.5_Intron|PEX5_ENST00000545220.1_3'UTR|PEX5_ENST00000266564.3_Silent_p.S231S|PEX5_ENST00000420616.2_Silent_p.S231S	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	231					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						CCCTGGAGTCCGGTGCAGGGT	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		-128	0.001		0.0	False		,,,				2504	0.0				p.S246S													.	.			0			c.C738T							C	,,,,	1,4405	2.1+/-5.4	0,1,2202	103.0	94.0	97.0		693,738,,693,693	2.8	1.0	12	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	PEX5	NM_000319.4,NM_001131023.1,NM_001131024.1,NM_001131025.1,NM_001131026.1	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	231/632,246/655,,231/640,231/640	7354887	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5830	exon8			GGAGTCCGGTGCA	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.693C>T	12.37:g.7354887C>T			Somatic	122	0	0		WXS	Illumina HiSeq	.	218	0.15	33	NM_001131023	311	0.06	18	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	37	CCDS44823.1																																																																																			0		0.582	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398611.1		NM_000319	
EIF2S3L	0	bcgsc.ca	37	12	10659228	10659228	+	Missense_Mutation	SNP	A	A	T	rs11053826	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:10659228A>T	ENST00000538173.1	+	1	740	c.727A>T	c.(727-729)Att>Ttt	p.I243F	EIF2S3L_ENST00000322446.3_Missense_Mutation_p.I243F			Q2VIR3	IF2GL_HUMAN		243	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.			I -> F (in Ref. 1; ABB92405). {ECO:0000305}.			GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation initiation factor activity (GO:0003743)			lung(8)	8						AGTAAAGAAAATTCCAGTACC	0.413													A|||	834	0.166534	0.0212	0.2032	5008	,	,		17381	0.1845		0.2266	False		,,,				2504	0.2566				.													Q5I0X0_HUMAN,NS,carcinoma,-1,2	.		2	0			.																																									SO:0001583	missense	0	.			AAGAAAATTCCAG																												ENST00000538173.1:c.727A>T	12.37:g.10659228A>T	ENSP00000445077:p.Ile243Phe		Somatic	541	0	0		WXS	Illumina HiSeq	Phase_1	893	0.05	42	.	239	0.00	0	Q5I0X0|Q6KF84	Missense_Mutation	SNP	ENST00000538173.1	37		352	0.16117216117216118	13	0.026422764227642278	71	0.19613259668508287	90	0.15734265734265734	178	0.23482849604221637	A	15.46	2.839784	0.51057	.	.	ENSG00000180574	ENST00000322446;ENST00000538173	T;T	0.72615	-0.67;-0.67	2.25	2.25	0.28309	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	.	.	.	.	.	.	.	.	.	.	.	.	T	0.05338	-1.0891	6	0.62326	D	0.03	.	8.0998	0.30850	1.0:0.0:0.0:0.0	rs11053826;rs11053826	.	.	.	F	243	ENSP00000323063:I243F;ENSP00000445077:I243F	ENSP00000323063:I243F	I	+	1	0	AC068775.1	10550495	1.000000	0.71417	0.998000	0.56505	0.868000	0.49771	3.289000	0.51747	1.048000	0.40298	0.254000	0.18369	ATT			0.413	EIF2S3L-002	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000400341.3			
TAS2R19	259294	ucsc.edu	37	12	11174765	11174765	+	Missense_Mutation	SNP	G	G	A	rs199722277		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:11174765G>A	ENST00000390673.2	-	1	454	c.406C>T	c.(406-408)Ccc>Tcc	p.P136S	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176888.1	NP_795369.1	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	136					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						AATACCAAGGGCCCCAACAGT	0.383																																					p.P136S													.	TAS2R19	30		0			c.C406T												96.0	90.0	92.0					12																	11174765		2203	4300	6503	SO:0001583	missense	259294	exon1			CCAAGGGCCCCAA	AX097730, AF494234	CCDS8640.1	12p13.2	2012-08-22			ENSG00000212124	ENSG00000212124		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19108	protein-coding gene	gene with protein product		613961	"""taste receptor, type 2, member 48"", ""taste receptor, type 2, member 23"""	TAS2R48, TAS2R23			Standard	NM_176888		Approved	T2R19, T2R23	uc010shj.2	P59542	OTTHUMG00000162687	ENST00000390673.2:c.406C>T	12.37:g.11174765G>A	ENSP00000375091:p.Pro136Ser		Somatic	99	0	0		RNA-Seq	Illumina HiSeq		169	0.01	1	NM_176888	30	0.43	13	Q3MIJ4|Q645X8	Missense_Mutation	SNP	ENST00000390673.2	37	CCDS8640.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.337760	0.00224	.	.	ENSG00000212124	ENST00000390673	T	0.29142	1.58	2.55	-5.1	0.02911	.	2.965530	0.03799	N	0.264155	T	0.10680	0.0261	N	0.02213	-0.635	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.29971	-0.9994	10	0.06494	T	0.89	.	8.043	0.30532	0.7191:0.0:0.1253:0.1556	.	136	P59542	T2R19_HUMAN	S	136	ENSP00000375091:P136S	ENSP00000375091:P136S	P	-	1	0	TAS2R19	11066032	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.751000	0.00792	-2.924000	0.00303	-1.111000	0.02071	CCC			0.383	TAS2R19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000370080.1		NM_176888	
HEBP1	50865	broad.mit.edu	37	12	13154583	13154583	+	5'Flank	DEL	G	G	-	rs398076428|rs59113920	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:13154583delG	ENST00000014930.4	-	0	0				RP11-377D9.3_ENST00000543321.1_lincRNA|HEBP1_ENST00000536942.1_5'Flank	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						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)		TCTGCTGAGCGGGGGCCCCCG	0.731													GGGG|GGGGG|GGGG|insertion	2433	0.485823	0.3949	0.4986	5008	,	,		11429	0.378		0.6064	False		,,,				2504	0.5869				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			CTGAGCGGGGGCC	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		12.37:g.13154583delG	Exception_encountered		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	0.50	5	.	0		0	A8K1G2|Q9Y5Z5	RNA	DEL	ENST00000014930.4	37	CCDS31749.1																																																																																					0.731	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401001.1			
KRAS	3845	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	rs121913527		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|KRAS_ENST00000557334.1_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.A146T	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,colon,carcinoma,+1,137	KRAS_ENST00000256078	1	137	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	c.G436A												207.0	188.0	195.0					12																	25378562		2203	4300	6503	SO:0001583	missense	3845	exon4	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TCTTTGCTGATGT	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr		Somatic	74	0.0135135135	1		WXS	Illumina HiSeq	.	134	0.19	26	NM_004985	262	0.19	49	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA			0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000412232.1		NM_033360	
Unknown	0	bcgsc.ca	37	12	27292934	27292934	+	IGR	SNP	G	G	C	rs3759122	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:27292934G>C								C12orf71 (57487 upstream) : RP11-582E3.2 (8281 downstream)																							AAACTCAGAAGTTGGATCTGA	0.353													G|||	949	0.189497	0.329	0.1297	5008	,	,		17967	0.1042		0.1501	False		,,,				2504	0.1718				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCAGAAGTTGGAT																													12.37:g.27292934G>C			Somatic	143	0	0		WXS	Illumina HiSeq	Phase_1	240	0.05	13	.	10	0.00	0		RNA	SNP		37																																																																																					0	0.353										
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40823354	40823354	+	Missense_Mutation	SNP	G	G	C	rs11564245	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:40823354G>C	ENST00000454784.4	+	14	1388	c.655G>C	c.(655-657)Gat>Cat	p.D219H	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	219			D -> H (in dbSNP:rs11564245).		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						CACATGCCAAGATGCAAAGTG	0.368													G|||	249	0.0497204	0.0129	0.0634	5008	,	,		20391	0.0208		0.1421	False		,,,				2504	0.0245				.													.	.			0			.																																									SO:0001583	missense	283463	.			TGCCAAGATGCAA	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.655G>C	12.37:g.40823354G>C	ENSP00000476404:p.Asp219His		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_1	93	0.08	7	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		148	0.06776556776556776	6	0.012195121951219513	23	0.06353591160220995	8	0.013986013986013986	111	0.14643799472295516	G	14.74	2.624257	0.46840	.	.	ENSG00000205592	ENST00000425730	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	T	0.00328	0.0010	N	0.25245	0.725	0.09310	P	1.0	.	.	.	.	.	.	T	0.11470	-1.0586	5	0.44086	T	0.13	.	11.7211	0.51683	0.0819:0.0:0.9181:0.0	rs11564245;rs17587037;rs52803223;rs11564245	.	.	.	H	448	.	ENSP00000395253:D448H	D	+	1	0	MUC19	39109621	1.000000	0.71417	0.997000	0.53966	0.624000	0.37722	2.664000	0.46783	2.619000	0.88677	0.460000	0.39030	GAT			0.368	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	40826514	40826514	+	Silent	SNP	T	T	C	rs10506162	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	149	0	0		WXS	Illumina HiSeq	Phase_1	168	0.12	20	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_1	179	0.16	29	.	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;mdanderson.org	37	12	40837898	40837898	+	Missense_Mutation	SNP	G	G	A	rs11564109	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_1	112	0.10	11	.	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	ucsc.edu	37	12	40921902	40921902	+	3'UTR	SNP	C	C	T	rs4768287	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:40921902C>T	ENST00000474954.1	+	0	2911				MUC19_ENST00000454784.4_Intron			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric						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						CCCCTGGAAGCTTCAGCACAG	0.438													T|||	652	0.130192	0.3003	0.0951	5008	,	,		18093	0.0188		0.1501	False		,,,				2504	0.0194				.													.	.			0			.																																									SO:0001624	3_prime_UTR_variant	283463	.			TGGAAGCTTCAGC	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	ENST00000474954.1:c.*2908C>T	12.37:g.40921902C>T			Somatic	17	0	0		WXS	Illumina HiSeq		35	0.17	6	.	0		0	Q8NA85	Silent	SNP	ENST00000474954.1	37		305	0.13965201465201466	139	0.28252032520325204	35	0.09668508287292818	8	0.013986013986013986	123	0.16226912928759896	T	5.077	0.199799	0.09652	.	.	ENSG00000205592	ENST00000424466	.	.	.	1.69	0.495	0.16890	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34204	-0.9838	3	.	.	.	.	4.3357	0.11085	0.0:0.3943:0.0:0.6057	rs4768287	.	.	.	F	16	.	.	L	+	1	0	MUC19	39208169	0.002000	0.14202	0.000000	0.03702	0.331000	0.28603	-0.017000	0.12590	-0.246000	0.09611	-0.516000	0.04426	CTT			0.438	MUC19-006	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000134360.1		XM_003403524	
Unknown	0	bcgsc.ca	37	12	43964281	43964281	+	IGR	SNP	T	T	G	rs34593988|rs11831774	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:43964281T>G								ADAMTS20 (18557 upstream) : RP11-350F4.2 (148514 downstream)																							CTTCGTTGAGTGAATGCAATA	0.403													T|||	560	0.111821	0.2753	0.0735	5008	,	,		19178	0.0258		0.0755	False		,,,				2504	0.044				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTGAGTGAATGC																													12.37:g.43964281T>G			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_1	112	0.04	5	.	0		0		RNA	SNP		37																																																																																					0	0.403										
Unknown	0	bcgsc.ca	37	12	43965011	43965011	+	IGR	SNP	A	A	T	rs66501365	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_1	131	0.08	11	.	0		0		RNA	SNP		37																																																																																					0	0.423										
PLEKHA8P1	51054	broad.mit.edu;bcgsc.ca	37	12	45566862	45566867	+	RNA	DEL	TTTATT	TTTATT	-	rs7301571	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TTTATT	TTTATT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:45566862_45566867delTTTATT	ENST00000256692.5	-	0	1818_1823					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						tatttatttatttatttttattttta	0.286																																					.													.	PLEKHA8P1	38		0			.																																											0	.			TATTTATTTATTT	AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"""putative glycolipid transfer protein"""		"""pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"""	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			12.37:g.45566868_45566873delTTTATT			Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	0.29	13	.	0		0		RNA	DEL	ENST00000256692.5	37																																																																																						0.286	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000404814.1		NR_037144	
KRT86	3892	bcgsc.ca	37	12	52646139	52646139	+	Intron	SNP	G	G	A	rs146544749	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_1	104	0.08	8	.	0		0	P78387	RNA	SNP	ENST00000544024.1	37	CCDS41785.1																																																																																					0.642	KRT86-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				NM_002284	
VDAC1P5	10187	bcgsc.ca	37	12	55197244	55197244	+	IGR	SNP	C	C	T	rs11171086	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:55197244C>T								RP11-850F7.7 (116026 upstream) : MUCL1 (27058 downstream)																							AGAGTCTGAGCTTGTAAATTC	0.433													C|||	2367	0.472644	0.1203	0.536	5008	,	,		20583	0.8413		0.3996	False		,,,				2504	0.5992				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGAGCTTGTAA																													12.37:g.55197244C>T			Somatic	29	0	0		WXS	Illumina HiSeq	Phase_1	42	0.17	7	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.433										
PHC1P1	653441	bcgsc.ca	37	12	55805647	55805647	+	IGR	SNP	A	A	G	rs12825123	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	335	0.0029850746	1		WXS	Illumina HiSeq	Phase_1	369	0.04	14	.	3798	0.00	1		RNA	SNP		37																																																																																					0	0.483										
RP11-415I12.3	0	bcgsc.ca	37	12	64118558	64118558	+	RNA	SNP	A	A	G	rs3864455	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:64118558A>G	ENST00000509615.2	-	0	238																											CTCATCAGTTAATTCTGGTAG	0.393													G|||	2986	0.596246	0.4629	0.5807	5008	,	,		19886	0.8403		0.4851	False		,,,				2504	0.6503				.													.	.			0			.																																											0	.			TCAGTTAATTCTG																													12.37:g.64118558A>G			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_1	128	0.08	10	.	1	0.00	0		Splice_Site	SNP	ENST00000509615.2	37																																																																																						0.393	RP11-415I12.3-001	KNOWN	basic	antisense	antisense		OTTHUMT00000400798.1			
SLC5A8	160728	hgsc.bcm.edu	37	12	101603313	101603313	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr12:101603313G>T	ENST00000536262.2	-	1	872	c.314C>A	c.(313-315)cCg>cAg	p.P105Q		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GTAGAACACCGGGAGGAAGAC	0.592																																					p.P105Q	GBM(60;420 1056 13605 22380 47675)												SLC5A8,colon,carcinoma,0,1	SLC5A8	0	1	0			c.C314A												43.0	38.0	39.0					12																	101603313		2203	4300	6503	SO:0001583	missense	160728	exon1			AACACCGGGAGGA	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.314C>A	12.37:g.101603313G>T	ENSP00000445340:p.Pro105Gln		Somatic	79	0.0126582278	1		WXS	Illumina HiSeq	.	95	0.05	5	NM_145913	0		0		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.593895	0.86953	.	.	ENSG00000256870	ENST00000536262	D	0.88354	-2.37	5.49	5.49	0.81192	.	0.047393	0.85682	D	0.000000	D	0.96445	0.8840	H	0.95470	3.675	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.97350	0.9963	10	0.87932	D	0	.	19.4145	0.94689	0.0:0.0:1.0:0.0	.	105	Q8N695	SC5A8_HUMAN	Q	105	ENSP00000445340:P105Q	ENSP00000445340:P105Q	P	-	2	0	SLC5A8	100127444	1.000000	0.71417	0.451000	0.26982	0.820000	0.46376	9.869000	0.99810	2.600000	0.87896	0.485000	0.47835	CCG			0.592	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000409401.1		NM_145913	
Unknown	0	bcgsc.ca	37	12	106566174	106566174	+	IGR	SNP	A	A	C	rs3853777	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	79	0	0		WXS	Illumina HiSeq	Phase_1	85	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.448										
UBE2L5P	171222	bcgsc.ca	37	13	31002373	31002373	+	IGR	SNP	G	G	A	rs2892546	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr13:31002373G>A								LINC01058 (5999 upstream) : HMGB1 (30510 downstream)																							TCGACGAAAAGGGGCAGGTCT	0.478													.|||	1543	0.308107	0.1641	0.2723	5008	,	,		18869	0.376		0.3877	False		,,,				2504	0.3763				.													.	.			0			.																																									SO:0001628	intergenic_variant	171222	.			CGAAAAGGGGCAG																													13.37:g.31002373G>A			Somatic	190	0	0		WXS	Illumina HiSeq	Phase_1	127	0.05	6	.	0		0		RNA	SNP		37																																																																																					0	0.478										
PPP1R2P10	100128626	bcgsc.ca	37	13	64385632	64385632	+	IGR	SNP	C	C	T	rs12429435	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr13:64385632C>T								RNU6-81P (27595 upstream) : RP11-394A14.2 (17347 downstream)																							AGCTCCTCCTCGACACTCCCG	0.517													C|||	305	0.0609026	0.0129	0.1254	5008	,	,		18092	0.0556		0.0974	False		,,,				2504	0.0481				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128626	.			CCTCCTCGACACT																													13.37:g.64385632C>T			Somatic	65	0	0		WXS	Illumina HiSeq	Phase_1	51	0.12	6	.	12	0.00	0		RNA	SNP		37																																																																																					0	0.517										
LGMNP1	122199	bcgsc.ca	37	13	65532930	65532930	+	IGR	SNP	A	A	G	rs9598891	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	61	0	0		WXS	Illumina HiSeq	Phase_1	33	0.18	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.453										
MTCL1P1	100288130	bcgsc.ca	37	13	71498338	71498338	+	IGR	SNP	C	C	T	rs7335663	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	78	0	0		WXS	Illumina HiSeq	Phase_1	74	0.08	6	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	81	0	0		WXS	Illumina HiSeq	Phase_1	72	0.06	4	.	0		0		RNA	SNP		37																																																																																					0	0.622										
PTMAP5	150928	bcgsc.ca;mdanderson.org	37	13	82264343	82264343	+	RNA	SNP	A	A	G	rs7326041	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr13:82264343A>G	ENST00000607242.1	+	0	298									prothymosin, alpha pseudogene 5																		GGGAGCAGGAAGCTGACAGTg	0.488													G|||	3140	0.626997	0.6399	0.6585	5008	,	,		16817	0.4583		0.6312	False		,,,				2504	0.7566				.													.	.			0			.																																											150928	.			GCAGGAAGCTGAC	S38627		13q13.1	2008-11-06	2008-04-03		ENSG00000214182	ENSG00000214182			9628	pseudogene	pseudogene	"""gene sequence 150"""		"""prothymosin, alpha pseudogene 5 (gene sequence 150)"""			1612591	Standard	NG_004798		Approved				OTTHUMG00000017147		13.37:g.82264343A>G			Somatic	136	0	0		WXS	Illumina HiSeq	Phase_1	108	0.12	13	.	38	0.89	34		RNA	SNP	ENST00000607242.1	37																																																																																						0.488	PTMAP5-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000470311.1			
PTMAP5	150928	bcgsc.ca	37	13	82264468	82264468	+	RNA	SNP	G	G	A	rs9574945	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr13:82264468G>A	ENST00000607242.1	+	0	423									prothymosin, alpha pseudogene 5																		ACGGGCAAGCGGGCAGCTGAA	0.478													G|||	2686	0.536342	0.5121	0.5807	5008	,	,		16562	0.4583		0.502	False		,,,				2504	0.6534				.													.	.			0			.																																											150928	.			GCAAGCGGGCAGC	S38627		13q13.1	2008-11-06	2008-04-03		ENSG00000214182	ENSG00000214182			9628	pseudogene	pseudogene	"""gene sequence 150"""		"""prothymosin, alpha pseudogene 5 (gene sequence 150)"""			1612591	Standard	NG_004798		Approved				OTTHUMG00000017147		13.37:g.82264468G>A			Somatic	56	0	0		WXS	Illumina HiSeq	Phase_1	35	0.11	4	.	605	0.00	0		RNA	SNP	ENST00000607242.1	37																																																																																						0.478	PTMAP5-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000470311.1			
PEX12P1	121727	bcgsc.ca	37	13	90644911	90644911	+	IGR	SNP	G	G	A	rs9588829	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	87	0	0		WXS	Illumina HiSeq	Phase_1	60	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.493										
MYO16	23026	broad.mit.edu	37	13	109793111	109793111	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr13:109793111delC	ENST00000357550.2	+	31	4526	c.4485delC	c.(4483-4485)ttcfs	p.F1495fs	MYO16_ENST00000356711.2_Frame_Shift_Del_p.F1495fs	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGCTGGTGTTCCCCCCGACCC	0.736																																					p.F1517fs													.	MYO16	285		0			c.4551delC												5.0	7.0	6.0					13																	109793111		2044	4076	6120	SO:0001589	frameshift_variant	23026	exon32			GGTGTTCCCCCCG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4485delC	13.37:g.109793111delC	ENSP00000350160:p.Phe1495fs		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	2242	0.01	13	NM_001198950	7	0.00	0		Frame_Shift_Del	DEL	ENST00000357550.2	37	CCDS32008.1																																																																																					0.736	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045746.1		NM_015011	
POTEG	404785	bcgsc.ca;mdanderson.org	37	14	19566036	19566036	+	Silent	SNP	C	C	T	rs77791636		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:19566036C>T	ENST00000409832.3	+	6	1132	c.1080C>T	c.(1078-1080)taC>taT	p.Y360Y	CTD-2311B13.5_ENST00000548748.1_lincRNA|RNU6-1239P_ENST00000391310.1_RNA	NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	360										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						TTTCTGACTACAAAGAAAAAC	0.289																																					p.Y360Y													.	POTEG	118		0			c.C1080T												69.0	81.0	77.0					14																	19566036		1508	2691	4199	SO:0001819	synonymous_variant	404785	exon6			TGACTACAAAGAA		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.1080C>T	14.37:g.19566036C>T			Somatic	360	0	0		WXS	Illumina HiSeq	Phase_1	227	0.10	23	NM_001005356	0		0	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																					0.289	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000408579.1		NM_001005356	
OR11H13P	440159	bcgsc.ca	37	14	19806717	19806717	+	IGR	SNP	A	A	C	rs1575832	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:19806717A>C								RP11-496I2.2 (63973 upstream) : RP11-146E13.4 (5458 downstream)																							GGACAATAGTATAGGATCCAA	0.423																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	440153	.			AATAGTATAGGAT																													14.37:g.19806717A>C			Somatic	476	0.0042016807	2		WXS	Illumina HiSeq	Phase_1	379	0.11	40	.	0		0		RNA	SNP		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	14	22070355	22070355	+	IGR	SNP	T	T	C	rs199637760		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	154	0	0		WXS	Illumina HiSeq	Phase_1	128	0.09	11	.	0		0		RNA	SNP		37																																																																																					0	0.507										
TTC6	319089	bcgsc.ca;mdanderson.org	37	14	38277999	38277999	+	Missense_Mutation	SNP	C	C	T	rs4901284	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:38277999C>T	ENST00000476979.1	+	6	706	c.419C>T	c.(418-420)aCa>aTa	p.T140I	TTC6_ENST00000553443.1_Missense_Mutation_p.T1506I|TTC6_ENST00000267368.7_Missense_Mutation_p.T140I|TTC6_ENST00000382320.3_Missense_Mutation_p.T220I			Q86TZ1	TTC6_HUMAN	tetratricopeptide repeat domain 6	140			T -> I (in dbSNP:rs4901284).							central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	14	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;1.59e-06)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0543)|all cancers(34;0.108)|BRCA - Breast invasive adenocarcinoma(188;0.156)|LUSC - Lung squamous cell carcinoma(13;0.176)	GBM - Glioblastoma multiforme(112;0.00551)		AATAGTTATACAGCATTTTAT	0.279													T|||	1469	0.293331	0.143	0.5058	5008	,	,		15983	0.0873		0.3857	False		,,,				2504	0.4632				.													.	.			0			.							T		762,3636	749.5+/-412.0	69,624,1506	125.0	130.0	128.0			4.5	0.4	14	dbSNP_111	128	3239,5287	639.2+/-399.4	620,1999,1644	no	near-gene-5				689,2623,3150	TT,TC,CC		37.9897,17.3261,30.9579			38277999	4001,8923	2199	4263	6462	SO:0001583	missense	319089	.			GTTATACAGCATT	BC014342		14q13.1	2013-01-10			ENSG00000139865	ENSG00000139865		"""Tetratricopeptide (TTC) repeat domain containing"""	19739	protein-coding gene	gene with protein product			"""non-protein coding RNA 291"", ""chromosome 14 open reading frame 25"""	NCRNA00291, C14orf25			Standard	XM_006709976		Approved		uc001wuj.3	Q86TZ1	OTTHUMG00000157369	ENST00000476979.1:c.419C>T	14.37:g.38277999C>T	ENSP00000417788:p.Thr140Ile		Somatic	503	0	0		WXS	Illumina HiSeq	Phase_1	388	0.05	18	.	0		0	Q3SY88|Q96CE6	Missense_Mutation	SNP	ENST00000476979.1	37		566	0.2591575091575092	64	0.13008130081300814	173	0.47790055248618785	37	0.06468531468531469	292	0.38522427440633245	T	1.283	-0.609768	0.03690	0.173261	0.379897	ENSG00000139865	ENST00000553443;ENST00000476979;ENST00000267368;ENST00000382320	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.62	4.48	0.54585	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.827656	0.10901	N	0.621644	T	0.00012	0.0000	.	.	.	0.20307	P	0.999917	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.44772	-0.9306	8	0.32370	T	0.25	-2.9234	7.7041	0.28640	0.0:0.1719:0.0:0.8281	rs4901284;rs17768684;rs60441984;rs4901284	1506;140	G3V3A5;Q86TZ1	.;TTC6_HUMAN	I	1506;140;140;220	ENSP00000451131:T1506I;ENSP00000417788:T140I;ENSP00000267368:T140I;ENSP00000371757:T220I	ENSP00000267368:T140I	T	+	2	0	TTC6	37347750	0.837000	0.29446	0.368000	0.25939	0.923000	0.55619	1.123000	0.31308	0.432000	0.26286	-0.516000	0.04426	ACA			0.279	TTC6-002	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000348621.2		XM_002343299	
BLZF2P	317729	bcgsc.ca	37	14	69335445	69335445	+	IGR	SNP	G	G	A	rs75789840	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:69335445G>A								RN7SL224P (22673 upstream) : ACTN1 (5414 downstream)																							ATTGACATACGTTCTGTTTGG	0.378													-|||	1379	0.275359	0.1581	0.4524	5008	,	,		18155	0.1835		0.3499	False		,,,				2504	0.3262				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACATACGTTCTGT																													14.37:g.69335445G>A			Somatic	19	0	0		WXS	Illumina HiSeq	Phase_1	16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.378										
AL133373.1	0	broad.mit.edu	37	14	92040590	92040590	+	Frame_Shift_Del	DEL	C	C	-	rs34650717	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:92040590delC	ENST00000596306.1	-	1	793	c.367delG	c.(367-369)gagfs	p.E123fs																								Tcgggcgcctccgccccgcgc	0.736													CC|CC|C|deletion	2499	0.499002	0.4493	0.621	5008	,	,		12978	0.5179		0.4881	False		,,,				2504	0.4714				.													.	.			0			.									991,1125		318,355,385	3.0	4.0	3.0			0.5	0.0	14	dbSNP_126	5	2231,2317		695,841,738	no	intergenic				1013,1196,1123	A1A1,A1R,RR		49.0545,46.8336,48.3493			92040590	3222,3442	890	1912	2802	SO:0001589	frameshift_variant	0	.			GCGCCTCCGCCCC																												ENST00000596306.1:c.367delG	14.37:g.92040590delC	ENSP00000472226:p.Glu123fs		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	40	0.18	7	.	0		0		Frame_Shift_Del	DEL	ENST00000596306.1	37																																																																																						0.736	AL133373.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding					
IGHG4	3503	bcgsc.ca	37	14	106091329	106091329	+	RNA	SNP	G	G	C	rs8015545	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:106091329G>C	ENST00000390543.2	-	0	564							P01861	IGHG4_HUMAN	immunoglobulin heavy constant gamma 4 (G4m 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)										TCCTGGTGCAGGACGGTGAGG	0.572													N|||	1226	0.244808	0.0159	0.2003	5008	,	,		27355	0.5238		0.2913	False		,,,				2504	0.2505				.													.	.			0			.							C		291,4097		2,287,1905	262.0	320.0	301.0			-4.1	0.0	14	dbSNP_116	301	2480,6092		6,2468,1812	no	intergenic				8,2755,3717	CC,CG,GG		28.9314,6.6317,21.3812			106091329	2771,10189	2194	4286	6480			3503	.			GGTGCAGGACGGT	K01316		14q32.33	2012-10-02			ENSG00000211892	ENSG00000211892		"""Immunoglobulins / IGH locus"""	5528	other	immunoglobulin gene		147130					Standard	NG_001019		Approved			P01861	OTTHUMG00000152481		14.37:g.106091329G>C			Somatic	252	0	0		WXS	Illumina HiSeq	Phase_1	172	0.05	9	.	1483	0.00	1		RNA	SNP	ENST00000390543.2	37																																																																																						0.572	IGHG4-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326390.1		NG_001019	
IGHG4	3503	bcgsc.ca	37	14	106092152	106092152	+	RNA	SNP	G	G	A	rs10137020	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:106092152G>A	ENST00000390543.2	-	0	251							P01861	IGHG4_HUMAN	immunoglobulin heavy constant gamma 4 (G4m 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)										TGTGATCTACGTTGCAGGTGT	0.607													N|||	1494	0.298323	0.0265	0.2637	5008	,	,		23764	0.5188		0.4394	False		,,,				2504	0.318				.													.	.			0			.							G		405,3811		44,317,1747	200.0	238.0	225.0			-4.6	0.0	14	dbSNP_119	225	3894,4606		885,2124,1241	no	intergenic				929,2441,2988	AA,AG,GG		45.8118,9.6063,33.8078			106092152	4299,8417	2108	4250	6358			3503	.			ATCTACGTTGCAG	K01316		14q32.33	2012-10-02			ENSG00000211892	ENSG00000211892		"""Immunoglobulins / IGH locus"""	5528	other	immunoglobulin gene		147130					Standard	NG_001019		Approved			P01861	OTTHUMG00000152481		14.37:g.106092152G>A			Somatic	137	0	0		WXS	Illumina HiSeq	Phase_1	92	0.07	6	.	592	0.00	0		RNA	SNP	ENST00000390543.2	37																																																																																						0.607	IGHG4-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326390.1		NG_001019	
IGHG2	3501	bcgsc.ca	37	14	106110137	106110137	+	RNA	SNP	C	C	T	rs8009156	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:106110137C>T	ENST00000390545.2	-	0	480							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)										TGCACCTCCACGCCGTCCACG	0.612													N|||	1493	0.298123	0.0174	0.2622	5008	,	,		22765	0.5337		0.4384	False		,,,				2504	0.316				.													.	.			0			.							C		379,3981		29,321,1830	209.0	186.0	193.0			-1.0	0.0	14	dbSNP_116	193	3874,4674		869,2136,1269	no	intergenic				898,2457,3099	TT,TC,CC		45.3205,8.6927,32.9486			106110137	4253,8655	2180	4274	6454			3501	.			CCTCCACGCCGTC	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.106110137C>T			Somatic	259	0	0		WXS	Illumina HiSeq	Phase_1	150	0.07	10	.	11907	0.00	9	A6NE66	RNA	SNP	ENST00000390545.2	37																																																																																						0.612	IGHG2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326391.1		NG_001019	
IGHGP	3505	bcgsc.ca	37	14	106134806	106134806	+	IGR	SNP	G	G	A	rs10144746	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:106134806G>A								RP11-731F5.2 (19412 upstream) : AL928768.3 (35494 downstream)																							GATGTCGCTGGGGTAGAAGCC	0.597													N|||	1577	0.314896	0.0189	0.2882	5008	,	,		23184	0.5367		0.4632	False		,,,				2504	0.3528				.													.	.			0			.																																									SO:0001628	intergenic_variant	3505	.			TCGCTGGGGTAGA																													14.37:g.106134806G>A			Somatic	359	0	0		WXS	Illumina HiSeq	Phase_1	266	0.04	11	.	6195	0.00	2		RNA	SNP		37																																																																																					0	0.597										
IGHV5-51	28388	bcgsc.ca;mdanderson.org	37	14	107035142	107035142	+	RNA	SNP	G	G	A	rs61732461	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	103	0	0		WXS	Illumina HiSeq	Phase_1	91	0.09	8	.	1397	0.00	0		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	
IGHV1-69	28461	bcgsc.ca;mdanderson.org	37	14	107170207	107170207	+	RNA	SNP	C	C	T	rs11845287	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	116	0	0		WXS	Illumina HiSeq	Phase_1	86	0.08	7	.	1341	0.01	8		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	
IGHV2-70	28454	bcgsc.ca	37	14	107178941	107178941	+	RNA	SNP	T	T	A	rs10133751	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:107178941T>A	ENST00000390634.2	-	0	311									immunoglobulin heavy variable 2-70																		TGTGCTGTAGTATTTATCATC	0.522																																					.													.	.			0			.												186.0	142.0	157.0					14																	107178941		2064	4177	6241			28454	.			CTGTAGTATTTAT	L21969		14q32.33	2012-02-08			ENSG00000211974	ENSG00000211974		"""Immunoglobulins / IGH locus"""	5577	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151870		14.37:g.107178941T>A			Somatic	334	0.005988024	2		WXS	Illumina HiSeq	Phase_1	261	0.05	12	.	393	0.01	5		RNA	SNP	ENST00000390634.2	37																																																																																						0.522	IGHV2-70-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324215.1		NG_001019	
IGHV2-70	28454	bcgsc.ca	37	14	107179013	107179013	+	RNA	SNP	A	A	G	rs61732216	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	251	0	0		WXS	Illumina HiSeq	Phase_1	200	0.05	10	.	440	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	
IGHV2-70	28454	bcgsc.ca	37	14	107179017	107179017	+	RNA	SNP	A	A	G	rs61732209	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:107179017A>G	ENST00000390634.2	-	0	235									immunoglobulin heavy variable 2-70																		CAGCTCACACACATTCCACTA	0.547													.|||	436	0.0870607	0.2239	0.0418	5008	,	,		13743	0.0565		0.0209	False		,,,				2504	0.0337				.													.	.			0			.							G		2002,2136		254,1494,321	102.0	82.0	89.0			0.6	0.0	14	dbSNP_129	89	2812,5524		82,2648,1438	no	intergenic				336,4142,1759	GG,GA,AA		33.7332,48.3809,38.5923			107179017	4814,7660	2069	4168	6237			28454	.			TCACACACATTCC	L21969		14q32.33	2012-02-08			ENSG00000211974	ENSG00000211974		"""Immunoglobulins / IGH locus"""	5577	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151870		14.37:g.107179017A>G			Somatic	248	0	0		WXS	Illumina HiSeq	Phase_1	196	0.04	8	.	468	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	
IGHV2-70	28454	bcgsc.ca	37	14	107179106	107179106	+	RNA	SNP	C	C	T	rs10144703	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr14:107179106C>T	ENST00000390634.2	-	0	146									immunoglobulin heavy variable 2-70																		ACCAGACTCCCTCAAGGTGAC	0.507																																					.													.	.			0			.							T		1909,2089		217,1475,307	66.0	54.0	58.0			0.3	0.2	14	dbSNP_119	58	2696,5624		75,2546,1539	no	intergenic				292,4021,1846	TT,TC,CC		32.4038,47.7489,37.3843			107179106	4605,7713	1999	4160	6159			28454	.			GACTCCCTCAAGG	L21969		14q32.33	2012-02-08			ENSG00000211974	ENSG00000211974		"""Immunoglobulins / IGH locus"""	5577	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151870		14.37:g.107179106C>T			Somatic	175	0	0		WXS	Illumina HiSeq	Phase_1	134	0.05	7	.	385	0.00	0		RNA	SNP	ENST00000390634.2	37																																																																																						0.507	IGHV2-70-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324215.1		NG_001019	
Unknown	0	bcgsc.ca	37	15	20445987	20445987	+	IGR	SNP	C	C	T	rs4931804	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:20445987C>T								RP11-173D3.1 (92781 upstream) : CHEK2P2 (42009 downstream)														p.V433I(1)									TGAACCTCAACGGGGGCGTTC	0.502																																					.													ENSG00000215407,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	stomach(1)	.																																									SO:0001628	intergenic_variant	0	.			CCTCAACGGGGGC																													15.37:g.20445987C>T			Somatic	202	0.004950495	1		WXS	Illumina HiSeq	Phase_1	227	0.04	8	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	15	20453913	20453913	+	IGR	SNP	C	C	T	rs2601516	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	166	0.0060240964	1		WXS	Illumina HiSeq	Phase_1	169	0.06	10	.	0		0		RNA	SNP		37																																																																																					0	0.612										
NBEAP1	606	bcgsc.ca	37	15	20867370	20867370	+	RNA	SNP	T	T	C	rs7402675	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:20867370T>C	ENST00000556948.1	-	0	3036							P0C6P0	BCL8_HUMAN	neurobeachin pseudogene 1																		CTGTAGCACATCATGAATATT	0.294																																					.													.	.			0			.																																											606	.			AGCACATCATGAA			15q11.2	2014-03-20	2011-05-03	2011-05-03	ENSG00000258590	ENSG00000258590			1007	pseudogene	pseudogene		601889	"""B-cell CLL/lymphoma 8"""	BCL8		9159141	Standard	NR_027992		Approved	BCL8A	uc010tze.1	P0C6P0	OTTHUMG00000171717		15.37:g.20867370T>C			Somatic	142	0	0		WXS	Illumina HiSeq	Phase_1	121	0.12	15	.	2	0.00	0		RNA	SNP	ENST00000556948.1	37																																																																																						0.294	NBEAP1-002	KNOWN	not_best_in_genome_evidence|basic	retained_intron	pseudogene		OTTHUMT00000414853.1		NR_027992	
NBEAP1	606	bcgsc.ca	37	15	20868281	20868281	+	RNA	SNP	T	T	C	rs11248797	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:20868281T>C	ENST00000556948.1	-	0	3036							P0C6P0	BCL8_HUMAN	neurobeachin pseudogene 1																		ATGAGCTGTTTCAGAAAAAGT	0.249																																					.													.	.			0			.																																											606	.			GCTGTTTCAGAAA			15q11.2	2014-03-20	2011-05-03	2011-05-03	ENSG00000258590	ENSG00000258590			1007	pseudogene	pseudogene		601889	"""B-cell CLL/lymphoma 8"""	BCL8		9159141	Standard	NR_027992		Approved	BCL8A	uc010tze.1	P0C6P0	OTTHUMG00000171717		15.37:g.20868281T>C			Somatic	627	0.0015948963	1		WXS	Illumina HiSeq	Phase_1	638	0.07	46	.	0		0		RNA	SNP	ENST00000556948.1	37																																																																																						0.249	NBEAP1-002	KNOWN	not_best_in_genome_evidence|basic	retained_intron	pseudogene		OTTHUMT00000414853.1		NR_027992	
Unknown	0	bcgsc.ca	37	15	22298230	22298230	+	IGR	SNP	A	A	T	rs8036276	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:22298230A>T								RP11-928F19.5 (98260 upstream) : RP11-69H14.6 (4953 downstream)																							CCATATCTCTAAAAAGGAGAA	0.443																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCTCTAAAAAGG																													15.37:g.22298230A>T			Somatic	192	0	0		WXS	Illumina HiSeq	Phase_1	207	0.04	9	.	0		0		RNA	SNP		37																																																																																					0	0.443										
Unknown	0	bcgsc.ca	37	15	22298333	22298333	+	IGR	SNP	A	A	T	rs1816290	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:22298333A>T								RP11-928F19.5 (98363 upstream) : RP11-69H14.6 (4850 downstream)																							GTCAGTGCATATGTTGTAGTG	0.433																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTGCATATGTTGT																													15.37:g.22298333A>T			Somatic	172	0	0		WXS	Illumina HiSeq	Phase_1	167	0.11	18	.	0		0		RNA	SNP		37																																																																																					0	0.433										
Unknown	0	bcgsc.ca	37	15	23500403	23500403	+	IGR	SNP	G	G	A	rs199579714		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:23500403G>A								GOLGA8EP (51983 upstream) : RP11-566K19.9 (73556 downstream)																							CGCACAGCACGGAAGTGTTTC	0.398																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGCACGGAAGTG																													15.37:g.23500403G>A			Somatic	155	0	0		WXS	Illumina HiSeq	Phase_1	146	0.07	10	.	0		0		RNA	SNP		37																																																																																					0	0.398										
RP11-143J24.1	0	bcgsc.ca	37	15	30297821	30297821	+	lincRNA	SNP	G	G	C	rs1004818	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:30297821G>C	ENST00000561392.1	-	0	309																											AATGAGAGATGAGATGCTGTG	0.438													C|||	3162	0.63139	0.7595	0.5706	5008	,	,		21179	0.4911		0.5984	False		,,,				2504	0.68				.													.	.			0			.																																											0	.			AGAGATGAGATGC																													15.37:g.30297821G>C			Somatic	70	0	0		WXS	Illumina HiSeq	Phase_1	59	0.08	5	.	0		0		RNA	SNP	ENST00000561392.1	37																																																																																						0.438	RP11-143J24.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000417288.1			
NUTM1	256646	hgsc.bcm.edu	37	15	34640735	34640735	+	Silent	SNP	T	T	C			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:34640735T>C	ENST00000333756.4	+	2	737	c.582T>C	c.(580-582)acT>acC	p.T194T	NUTM1_ENST00000438749.3_Silent_p.T212T|NUTM1_ENST00000537011.1_Silent_p.T222T	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	194						cytoplasm (GO:0005737)|nucleus (GO:0005634)											CTGTGGCCACTCTATCCAAGC	0.577																																					p.T194T													.	.			0			c.T582C												38.0	39.0	38.0					15																	34640735		2201	4298	6499	SO:0001819	synonymous_variant	256646	exon2			GGCCACTCTATCC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.582T>C	15.37:g.34640735T>C			Somatic	72	0	0		WXS	Illumina HiSeq	.	64	0.06	4	NM_175741	15	0.00	0	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Silent	SNP	ENST00000333756.4	37	CCDS32190.1																																																																																					0.577	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000418026.1		NM_175741	
Unknown	0	bcgsc.ca	37	15	35385338	35385338	+	IGR	SNP	T	T	C	rs386782961|rs12901760	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:35385338T>C								RP11-463I20.2 (81946 upstream) : RP11-323I15.5 (5884 downstream)																							gcggtggcggtggcccaggcg	0.622													T|||	3089	0.616813	0.5673	0.7262	5008	,	,		10313	0.4792		0.67	False		,,,				2504	0.6933				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGCGGTGGCCCA																													15.37:g.35385338T>C			Somatic	47	0	0		WXS	Illumina HiSeq	Phase_1	49	0.14	7	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.622										
HMGN1P26	100128015	bcgsc.ca	37	15	62654429	62654429	+	IGR	SNP	C	C	T	rs2089322	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	211	0	0		WXS	Illumina HiSeq	Phase_1	221	0.06	14	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.512										
CCDC33	80125	ucsc.edu;bcgsc.ca	37	15	74623054	74623054	+	Missense_Mutation	SNP	A	A	G			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:74623054A>G	ENST00000398814.3	+	13	1938	c.1507A>G	c.(1507-1509)Agg>Ggg	p.R503G	CCDC33_ENST00000321288.5_Missense_Mutation_p.R706G|CCDC33_ENST00000558821.1_Missense_Mutation_p.R96G|CCDC33_ENST00000268082.4_Missense_Mutation_p.R96G	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	706										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GAAGAAACTGAGGGACAGGGT	0.582																																					p.R503G													.	CCDC33	160		0			c.A1507G												82.0	83.0	83.0					15																	74623054		1992	4174	6166	SO:0001583	missense	80125	exon13			AAACTGAGGGACA	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1507A>G	15.37:g.74623054A>G	ENSP00000381795:p.Arg503Gly		Somatic	28	0	0		WXS	Illumina HiSeq		33	0.12	4	NM_025055	0		0	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.418805	0.62622	.	.	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.36340	1.26;1.64;1.37;1.37	4.28	0.208	0.15221	.	0.340466	0.28927	N	0.013689	T	0.51500	0.1678	M	0.76838	2.35	0.25139	N	0.990519	D;D;D;D	0.71674	0.975;0.99;0.979;0.998	P;P;P;D	0.66084	0.736;0.795;0.628;0.941	T	0.43637	-0.9379	10	0.87932	D	0	.	6.3479	0.21359	0.54:0.3152:0.0:0.1448	.	96;96;706;503	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	G	706;503;96;96	ENSP00000325012:R706G;ENSP00000381795:R503G;ENSP00000325661:R96G;ENSP00000268082:R96G	ENSP00000268082:R96G	R	+	1	2	CCDC33	72410107	1.000000	0.71417	0.988000	0.46212	0.874000	0.50279	1.079000	0.30766	-0.251000	0.09542	0.372000	0.22366	AGG			0.582	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000419491.2		NM_182791	
CSPG4P13	100302666	bcgsc.ca	37	15	78187053	78187053	+	IGR	SNP	G	G	C	rs144204249	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:78187053G>C								LINGO1 (75183 upstream) : CSPG4P13 (6949 downstream)																							GAACCACCTGGTCGGTCGGCT	0.627													G|||	47	0.00938498	0.0076	0.013	5008	,	,		15145	0.0		0.0249	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACCTGGTCGGTC																													15.37:g.78187053G>C			Somatic	187	0	0		WXS	Illumina HiSeq	Phase_1	159	0.08	13	.	0		0		RNA	SNP		37																																																																																					0	0.627										
ADAMTS7P3	400406	bcgsc.ca	37	15	78272318	78272318	+	IGR	SNP	C	C	G	rs12439777	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:78272318C>G								RP11-114H24.3 (16322 upstream) : RP11-114H24.5 (8015 downstream)																							AGCACCAGGGCCCTCCCCTCC	0.677																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAGGGCCCTCCC																													15.37:g.78272318C>G			Somatic	759	0.0065876153	5		WXS	Illumina HiSeq	Phase_1	717	0.10	70	.	0		0		RNA	SNP		37																																																																																					0	0.677										
Unknown	0	bcgsc.ca	37	15	79852289	79852289	+	IGR	SNP	A	A	G	rs1685164	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:79852289A>G								KIAA1024 (87657 upstream) : RNU6-667P (257401 downstream)																							CCCTCAGCACATTTAAGGCAT	0.517													G|||	3955	0.789736	0.7852	0.7695	5008	,	,		18328	0.9415		0.6064	False		,,,				2504	0.8425				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGCACATTTAAG																													15.37:g.79852289A>G			Somatic	96	0	0		WXS	Illumina HiSeq	Phase_1	88	0.09	8	.	0		0		RNA	SNP		37																																																																																					0	0.517										
Unknown	0	bcgsc.ca	37	15	82620272	82620272	+	IGR	SNP	A	A	T	rs141755317		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:82620272A>T								RP13-98N21.3 (22120 upstream) : GOLGA6L10 (14857 downstream)																							GGGGACTCCCACCTTCCCAAC	0.637													.|||	1964	0.392173	0.3737	0.2723	5008	,	,		12227	0.2133		0.4006	False		,,,				2504	0.6779				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACTCCCACCTTCC																													15.37:g.82620272A>T			Somatic	52	0	0		WXS	Illumina HiSeq	Phase_1	64	0.16	10	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.637										
Unknown	0	bcgsc.ca	37	15	84722797	84722798	+	IGR	DNP	TT	TT	GC	rs4559876|rs377507435|rs116443262	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TT	TT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr15:84722797_84722798TT>GC								ADAMTSL3 (14203 upstream) : EFTUD1P1 (26121 downstream)																							GGTCCCAAGCTTTATAATCGTC	0.347																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAAGCTTTATAA																													15.37:g.84722797_84722798delinsGC			Somatic	62	0	0		WXS	Illumina HiSeq	Phase_1	67	0.09	6	.	0		0		RNA	DNP		37																																																																																					0	0.347										
Unknown	0	bcgsc.ca	37	16	16463250	16463250	+	IGR	SNP	A	A	G	rs2376640	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr16:16463250A>G								AC138969.4 (18803 upstream) : NPIPA7 (9661 downstream)																							GGGCCACTGCAAAGAGTTCTG	0.657																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACTGCAAAGAGT																													16.37:g.16463250A>G			Somatic	101	0	0		WXS	Illumina HiSeq	Phase_1	83	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.657										
ITPRIPL2	162073	ucsc.edu	37	16	19126254	19126254	+	Silent	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr16:19126254C>T	ENST00000381440.3	+	1	1001	c.471C>T	c.(469-471)atC>atT	p.I157I	CTD-2349B8.1_ENST00000564808.2_3'UTR	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	157						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GAGACTTCATCCAGGTGGGCA	0.711																																					p.I157I													.	ITPRIPL2	40		0			c.C471T												11.0	13.0	12.0					16																	19126254		2139	4190	6329	SO:0001819	synonymous_variant	162073	exon1			CTTCATCCAGGTG		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.471C>T	16.37:g.19126254C>T			Somatic	39	0	0		RNA-Seq	Illumina HiSeq		25	0.12	3	NM_001034841	29	0.17	5		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																					0.711	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000435827.3		NM_001034841	
Unknown	0	bcgsc.ca	37	16	88620195	88620195	+	IGR	SNP	T	T	G	rs2879897	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr16:88620195T>G								ZFPM1 (16771 upstream) : ZC3H18 (16593 downstream)																							TTTATACACTTTCCATTAAAA	0.458													T|||	1932	0.385783	0.4319	0.4409	5008	,	,		19107	0.1687		0.5954	False		,,,				2504	0.2924				.													C16orf85,NS,carcinoma,0,1	.		1	0			.							T		1972,2424	554.5+/-379.0	460,1052,686	61.0	58.0	59.0			0.8	0.0	16	dbSNP_101	59	5133,3467	635.3+/-399.0	1520,2093,687	no	intergenic				1980,3145,1373	GG,GT,TT		40.314,44.859,45.3293			88620195	7105,5891	2198	4300	6498	SO:0001628	intergenic_variant	400555	.			TACACTTTCCATT																													16.37:g.88620195T>G			Somatic	85	0	0		WXS	Illumina HiSeq	Phase_1	53	0.09	5	.	0		0		Missense_Mutation	SNP		37		955	0.43727106227106227	217	0.4410569105691057	177	0.4889502762430939	98	0.17132867132867133	463	0.6108179419525066	T	5.710	0.315568	0.10789	0.44859	0.59686	ENSG00000205036	ENST00000378416	.	.	.	0.81	0.81	0.18732	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.44697	-0.9311	6	0.87932	D	0	.	3.8303	0.08871	0.0:0.0:0.0:1.0	rs2879897;rs52802375;rs59092101;rs2879897	145	Q6ZSH3	CP085_HUMAN	D	145	.	ENSP00000367672:E145D	E	-	3	2	C16orf85	87147696	0.985000	0.35326	0.041000	0.18516	0.033000	0.12548	0.909000	0.28558	0.585000	0.29608	0.164000	0.16699	GAA		0	0.458										
Unknown	0	bcgsc.ca;mdanderson.org	37	16	88633052	88633052	+	IGR	SNP	G	G	C	rs56983565	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr16:88633052G>C								ZFPM1 (29628 upstream) : ZC3H18 (3736 downstream)																							caagaacgctggcaggctaag	0.522													C|||	1763	0.352037	0.2368	0.3516	5008	,	,		19967	0.3671		0.4662	False		,,,				2504	0.3753				.													.	.			0			.							C		721,1923		105,511,706	90.0	79.0	83.0			0.2	0.0	16	dbSNP_129	83	2050,2568		453,1144,712	no	intergenic				558,1655,1418	CC,CG,GG		44.3915,27.2693,38.1575			88633052	2771,4491	1322	2309	3631	SO:0001628	intergenic_variant	400555	.			AACGCTGGCAGGC																													16.37:g.88633052G>C			Somatic	93	0	0		WXS	Illumina HiSeq	Phase_1	80	0.09	7	.	0		0		Missense_Mutation	SNP		37		840	0.38461538461538464	151	0.30691056910569103	151	0.4171270718232044	201	0.3513986013986014	337	0.4445910290237467	C	1.262	-0.615640	0.03663	0.272693	0.443915	ENSG00000205036	ENST00000378416	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.40496	-0.9560	5	0.87932	D	0	.	.	.	.	rs56983565;rs62050266	25	Q6ZSH3	CP085_HUMAN	R	25	.	ENSP00000367672:P25R	P	-	2	0	C16orf85	87160553	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.689000	0.01923	-0.685000	0.05177	-0.676000	0.03789	CCA		0	0.522										
RAP1GAP2	23108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	2921439	2921439	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr17:2921439C>T	ENST00000254695.8	+	18	1669	c.1579C>T	c.(1579-1581)Ctc>Ttc	p.L527F	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.L512F|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.L527F|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.L508F	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	527					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CCCTGGCAGCCTCAGCGGGGG	0.667																																					p.L527F													.	.			0			c.C1579T												16.0	19.0	18.0					17																	2921439		2088	4221	6309	SO:0001583	missense	23108	exon18			GGCAGCCTCAGCG	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1579C>T	17.37:g.2921439C>T	ENSP00000254695:p.Leu527Phe		Somatic	106	0	0		WXS	Illumina HiSeq	.	79	0.20	16	NM_015085	47	0.57	27	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.788730	0.31685	.	.	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56	4.66	4.66	0.58398	.	0.182769	0.49305	D	0.000149	D	0.92067	0.7486	M	0.70595	2.14	0.53688	D	0.999973	D;P	0.58268	0.982;0.947	P;P	0.61201	0.885;0.692	D	0.89528	0.3783	10	0.09338	T	0.73	-15.8435	16.9017	0.86115	0.0:1.0:0.0:0.0	.	512;527	Q684P5-2;Q684P5	.;RPGP2_HUMAN	F	527;512;508;527	ENSP00000254695:L527F;ENSP00000389824:L512F;ENSP00000439688:L508F;ENSP00000444890:L527F	ENSP00000254695:L527F	L	+	1	0	RAP1GAP2	2868189	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	4.556000	0.60775	2.320000	0.78422	0.462000	0.41574	CTC			0.667	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000438208.2			
FLII	2314	bcgsc.ca	37	17	18151320	18151320	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr17:18151320G>T	ENST00000327031.4	-	19	2443	c.2218C>A	c.(2218-2220)Ctg>Atg	p.L740M	FLII_ENST00000379450.4_Missense_Mutation_p.L654M|FLII_ENST00000545457.2_Missense_Mutation_p.L685M|FLII_ENST00000579294.1_Missense_Mutation_p.L729M|FLII_ENST00000578558.1_Intron	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	740	Interaction with ACTL6A.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					ATCTGTGGCAGCTCCAGGTAG	0.597											OREG0024225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L740M													.	FLII	79		0			c.C2218A												87.0	85.0	86.0					17																	18151320		2203	4300	6503	SO:0001583	missense	2314	exon19			GTGGCAGCTCCAG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.2218C>A	17.37:g.18151320G>T	ENSP00000324573:p.Leu740Met		Somatic	69	0	0	723	WXS	Illumina HiSeq	Phase_1	53	0.09	5	NM_002018	202	0.00	0	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.530774	0.64860	.	.	ENSG00000177731	ENST00000327031;ENST00000379450	T;T	0.14893	2.47;2.47	5.12	5.12	0.69794	.	0.075920	0.56097	D	0.000034	T	0.36082	0.0954	M	0.62088	1.915	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.97110	0.997;0.997;1.0;0.996	T	0.08576	-1.0715	10	0.87932	D	0	-13.0092	9.3562	0.38168	0.1596:0.0:0.8404:0.0	.	654;654;740;709	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	M	740;654	ENSP00000324573:L740M;ENSP00000368763:L654M	ENSP00000324573:L740M	L	-	1	2	FLII	18092045	1.000000	0.71417	1.000000	0.80357	0.566000	0.35808	5.421000	0.66447	2.385000	0.81259	0.561000	0.74099	CTG			0.597	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000132032.2		NM_002018	
POLRMTP1	284167	bcgsc.ca	37	17	60214681	60214681	+	IGR	SNP	G	G	A	rs12937135	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr17:60214681G>A								Y_RNA (14899 upstream) : TBC1D3P2 (127384 downstream)																							CCGTTCTTCTGCTTTCGTGTG	0.557													G|||	216	0.043131	0.0083	0.049	5008	,	,		18345	0.0		0.1223	False		,,,				2504	0.0491				.													.	.			0			.																																									SO:0001628	intergenic_variant	284167	.			TCTTCTGCTTTCG																													17.37:g.60214681G>A			Somatic	87	0	0		WXS	Illumina HiSeq	Phase_1	80	0.08	6	.	65	0.00	0		RNA	SNP		37																																																																																					0	0.557										
FBXO36P1	732538	bcgsc.ca	37	17	66091753	66091753	+	lincRNA	SNP	C	C	T	rs35320230	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr17:66091753C>T	ENST00000579629.1	-	0	1300																											ATAGTCCAGTCGATCTGCGAC	0.522													C|||	327	0.0652955	0.1014	0.0303	5008	,	,		21856	0.0417		0.0398	False		,,,				2504	0.092				.													.	.			0			.																																											732538	.			TCCAGTCGATCTG																													17.37:g.66091753C>T			Somatic	125	0	0		WXS	Illumina HiSeq	Phase_1	129	0.07	9	.	0		0		RNA	SNP	ENST00000579629.1	37																																																																																						0.522	AC145343.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000448121.1			
Unknown	0	bcgsc.ca	37	17	74591725	74591725	+	IGR	SNP	T	T	A	rs72867697	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr17:74591725T>A								ST6GALNAC2 (9515 upstream) : ST6GALNAC1 (29119 downstream)																							TAGATCTTAGTTTTCATTCCT	0.383													T|||	549	0.109625	0.0605	0.1772	5008	,	,		16561	0.0347		0.173	False		,,,				2504	0.1401				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTTAGTTTTCAT																													17.37:g.74591725T>A			Somatic	47	0	0		WXS	Illumina HiSeq	Phase_1	40	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.383										
SMCHD1	23347	ucsc.edu	37	18	2666989	2666989	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:2666989G>T	ENST00000320876.6	+	3	721	c.383G>T	c.(382-384)gGc>gTc	p.G128V	SMCHD1_ENST00000261598.8_Missense_Mutation_p.G128V	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	128					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GTTAAAAGTGGCATGTATGAA	0.378																																					p.G128V													.	SMCHD1	88		0			c.G383T												86.0	76.0	79.0					18																	2666989		1892	4124	6016	SO:0001583	missense	23347	exon3			AAAGTGGCATGTA	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.383G>T	18.37:g.2666989G>T	ENSP00000326603:p.Gly128Val		Somatic	124	0	0		RNA-Seq	Illumina HiSeq		95	0.02	2	NM_015295	68	0.12	8	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882461	0.91740	.	.	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.73152	-0.72;-0.68	5.56	5.56	0.83823	ATPase-like, ATP-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.79907	0.4527	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81052	-0.1107	10	0.87932	D	0	.	19.8772	0.96880	0.0:0.0:1.0:0.0	.	128	A6NHR9	SMHD1_HUMAN	V	128	ENSP00000326603:G128V;ENSP00000261598:G128V	ENSP00000261598:G128V	G	+	2	0	SMCHD1	2656989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.406000	0.97321	2.774000	0.95407	0.585000	0.79938	GGC			0.378	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000441082.2	rescued with RNA-seq		
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	2688481	2688483	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	TCT	TCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:2688481_2688483delTCT	ENST00000320876.6	+	6	1066_1068	c.728_730delTCT	c.(727-732)gtcttc>gtc	p.F245del	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_In_Frame_Del_p.F245del	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	245					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAGCAAGCTGTCTTCTTTGTTGG	0.35																																					p.243_243del													.	SMCHD1	88		0			c.727_729del																																									SO:0001651	inframe_deletion	23347	exon6			AAGCTGTCTTCTT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.728_730delTCT	18.37:g.2688484_2688486delTCT	ENSP00000326603:p.Phe245del		Somatic	116	0	0		WXS	Illumina HiSeq	.	89	0.11	10	NM_015295	104	0.00	0	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	In_Frame_Del	DEL	ENST00000320876.6	37	CCDS45822.1																																																																																					0.350	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000441082.2			
RPS10P27	100129556	bcgsc.ca	37	18	21252592	21252592	+	IGR	SNP	A	A	G	rs12962228	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:21252592A>G								ANKRD29 (9743 upstream) : LAMA3 (16814 downstream)																							TGAAGGTTGGACACATTCTTG	0.468													G|||	1826	0.364617	0.2118	0.3977	5008	,	,		20848	0.2103		0.6213	False		,,,				2504	0.4427				.													.	.			0			.																																									SO:0001628	intergenic_variant	100129556	.			GGTTGGACACATT																													18.37:g.21252592A>G			Somatic	17	0	0		WXS	Illumina HiSeq	Phase_1	9	0.33	3	.	0		0		RNA	SNP		37																																																																																					0	0.468										
AQP4	361	broad.mit.edu	37	18	24445878	24445878	+	5'Flank	DEL	T	T	-	rs68070007|rs3974653|rs529134198|rs56282359	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:24445878delT	ENST00000383168.4	-	0	0				AQP4-AS1_ENST00000578701.1_RNA|AQP4_ENST00000440832.3_5'Flank|AQP4-AS1_ENST00000582605.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000579964.1_RNA	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4						carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					ATTTACTTAATTTTTTTTTTT	0.299																																					.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			ACTTAATTTTTTT	U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"""Ion channels / Aquaporins"""	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955		18.37:g.24445878delT	Exception_encountered		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	9	0.33	3	.	0		0	P78564	RNA	DEL	ENST00000383168.4	37	CCDS11889.1																																																																																					0.299	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254914.2		NM_001650, NM_004028	
ARIH2P1	390844	bcgsc.ca	37	18	26232188	26232188	+	IGR	SNP	T	T	G	rs2655356	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:26232188T>G								CDH2 (474778 upstream) : RP11-510D21.1 (132843 downstream)																							CGTAGCTGCTTGGAGCAGCAC	0.537													G|||	3217	0.642372	0.8737	0.5259	5008	,	,		21040	0.6538		0.4771	False		,,,				2504	0.5706				.													.	.			0			.																																									SO:0001628	intergenic_variant	390844	.			GCTGCTTGGAGCA																													18.37:g.26232188T>G			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	33	0.12	4	.	0		0		RNA	SNP		37																																																																																					0	0.537										
NRBF2P1	648532	bcgsc.ca	37	18	33422218	33422218	+	IGR	SNP	A	A	T	rs61740693	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:33422218A>T								RP11-873E20.1 (124276 upstream) : MIR187 (62562 downstream)																							AAAGATGACAAAACAATTATA	0.403													A|||	1607	0.320887	0.3222	0.3343	5008	,	,		20565	0.2758		0.329	False		,,,				2504	0.3476				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGACAAAACAAT																													18.37:g.33422218A>T			Somatic	51	0	0		WXS	Illumina HiSeq	Phase_1	53	0.17	9	.	0		0		RNA	SNP		37																																																																																					0	0.403										
TPMTP1	400650	bcgsc.ca	37	18	45157181	45157181	+	IGR	SNP	T	T	C	rs3813071	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:45157181T>C								CTD-2130O13.1 (43221 upstream) : SMAD2 (200740 downstream)																							GGGGATTGACTATCTTTCTGA	0.299													T|||	810	0.161741	0.0363	0.17	5008	,	,		18974	0.256		0.173	False		,,,				2504	0.2168				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATTGACTATCTTT																													18.37:g.45157181T>C			Somatic	93	0	0		WXS	Illumina HiSeq	Phase_1	64	0.13	8	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.299										
FAUP1	140623	bcgsc.ca	37	18	72057474	72057474	+	IGR	SNP	A	A	G	rs11553061	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:72057474A>G								C18orf63 (31052 upstream) : RP11-231E4.2 (19208 downstream)																							CTGGGCGACCATTTCCTGGCC	0.602													G|||	822	0.164137	0.1543	0.1282	5008	,	,		17340	0.0714		0.2237	False		,,,				2504	0.2372				.													.	.			0			.																																									SO:0001628	intergenic_variant	140623	.			GCGACCATTTCCT																													18.37:g.72057474A>G			Somatic	26	0	0		WXS	Illumina HiSeq	Phase_1	20	0.20	4	.	24	0.83	20		RNA	SNP		37																																																																																					0	0.602										
KCNG2	26251	bcgsc.ca	37	18	77623903	77623903	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr18:77623903G>T	ENST00000316249.3	+	1	236	c.236G>T	c.(235-237)cGc>cTc	p.R79L		NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	79					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		TGCGCCTTCCGCGCCATCGTG	0.711																																					p.R79L													.	KCNG2	48		0			c.G236T												16.0	14.0	15.0					18																	77623903		2178	4276	6454	SO:0001583	missense	26251	exon1			CCTTCCGCGCCAT	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.236G>T	18.37:g.77623903G>T	ENSP00000315654:p.Arg79Leu		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_1	27	0.15	4	NM_012283	0		0		Missense_Mutation	SNP	ENST00000316249.3	37	CCDS12019.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917547	0.33815	.	.	ENSG00000178342	ENST00000316249	T	0.77877	-1.13	3.77	2.6	0.31112	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.221994	0.33438	U	0.004908	T	0.80994	0.4731	M	0.76170	2.325	0.42468	D	0.992814	P	0.46512	0.879	P	0.50659	0.647	T	0.81597	-0.0860	10	0.39692	T	0.17	.	12.0661	0.53588	0.1056:0.0:0.8944:0.0	.	79	Q9UJ96	KCNG2_HUMAN	L	79	ENSP00000315654:R79L	ENSP00000315654:R79L	R	+	2	0	KCNG2	75724891	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	6.582000	0.74049	1.676000	0.50930	0.478000	0.44815	CGC			0.711	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000103906.1		NM_012283	
ZNF849P	100130108	bcgsc.ca	37	19	22869030	22869030	+	RNA	SNP	G	G	A	rs78524936	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	436	0	0		WXS	Illumina HiSeq	Phase_1	415	0.06	24	.	2	0.00	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	154	0	0		WXS	Illumina HiSeq	Phase_1	132	0.06	8	.	3	0.00	0		Silent	SNP	ENST00000601860.1	37																																																																																						0.393	CTC-457E21.9-001	KNOWN	basic	antisense	antisense		OTTHUMT00000464586.1			
ZNF724P	440519	ucsc.edu;bcgsc.ca	37	19	23405580	23405580	+	Silent	SNP	T	T	C	rs10412126	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr19:23405580T>C	ENST00000418100.1	-	4	1584	c.1467A>G	c.(1465-1467)ctA>ctG	p.L489L				A8MTY0	ZN724_HUMAN	zinc finger protein 724, pseudogene	489					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						GGTGTGAGGATAGGTTAAAAG	0.383													N|||	2536	0.50639	0.1982	0.6398	5008	,	,		20851	0.6627		0.6014	False		,,,				2504	0.5695				.													ZNF724P_ENST00000418100,NS,carcinoma,0,2	.		2	0			.																																									SO:0001819	synonymous_variant	440519	.			TGAGGATAGGTTA			19p12	2014-02-14	2010-08-03		ENSG00000196081	ENSG00000196081			32460	pseudogene	pseudogene			"""zinc finger protein 724 pseudogene"", ""zinc finger protein 724 (pseudogene)"""				Standard	NR_045525		Approved		uc021uru.1	A8MTY0	OTTHUMG00000183231	ENST00000418100.1:c.1467A>G	19.37:g.23405580T>C			Somatic	25	0	0		WXS	Illumina HiSeq		29	0.14	4	.	70	0.00	0		Silent	SNP	ENST00000418100.1	37																																																																																						0.383	ZNF724P-001	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000465743.1			
MAN1A2P1	100129507	bcgsc.ca	37	19	29282028	29282028	+	IGR	SNP	T	T	C	rs7351076	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr19:29282028T>C								AC005307.3 (63441 upstream) : AC007795.1 (78674 downstream)																							ACTCATGACATGTATATGCAA	0.438													T|||	2196	0.438498	0.2065	0.5605	5008	,	,		21095	0.2808		0.6233	False		,,,				2504	0.638				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGACATGTATAT																													19.37:g.29282028T>C			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_1	27	0.15	4	.	0		0		RNA	SNP		37																																																																																					0	0.438										
CAPNS1	826	bcgsc.ca	37	19	36640664	36640669	+	Intron	DEL	GCTGGT	GCTGGT	-	rs145937393|rs17879265	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GCTGGT	GCTGGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr19:36640664_36640669delGCTGGT	ENST00000246533.3	+	11	1378				AD001527.7_ENST00000604228.1_RNA|CAPNS1_ENST00000587718.1_In_Frame_Del_p.LV303del|CAPNS1_ENST00000588780.1_Intron|CAPNS1_ENST00000589146.1_Intron|CAPNS1_ENST00000588815.1_Intron|CAPNS1_ENST00000590874.1_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			Somatic	115	0	0		WXS	Illumina HiSeq	Phase_1	102	0.06	6	.	1	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			
RUVBL2	10856	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	49502588	49502588	+	Missense_Mutation	SNP	A	A	G			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr19:49502588A>G	ENST00000595090.1	+	2	489	c.25A>G	c.(25-27)Aaa>Gaa	p.K9E	RUVBL2_ENST00000413176.2_5'UTR|RUVBL2_ENST00000598768.1_3'UTR|RUVBL2_ENST00000601968.1_5'UTR	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	9					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		AGCCACAACCAAAGTCCCGGA	0.547																																					p.K9E													.	.			0			c.A25G												136.0	146.0	143.0					19																	49502588		2069	4198	6267	SO:0001583	missense	10856	exon2			ACAACCAAAGTCC	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"""INO80 complex subunits"", ""ATPases / AAA-type"""	10475	protein-coding gene	gene with protein product	"""reptin"", ""INO80 complex subunit J"""	604788	"""RuvB (E coli homolog)-like 2"", ""RuvB-like 2 (E. coli)"""			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.25A>G	19.37:g.49502588A>G	ENSP00000473172:p.Lys9Glu		Somatic	206	0	0		WXS	Illumina HiSeq	.	204	0.17	34	NM_006666	384	0.35	133	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.451196	0.43531	.	.	ENSG00000183207	ENST00000221413	T	0.49432	0.78	3.58	3.58	0.41010	.	0.000000	0.85682	U	0.000000	T	0.36853	0.0982	L	0.38649	1.16	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.13407	0.008;0.009	T	0.30851	-0.9964	10	0.52906	T	0.07	-26.3814	10.7768	0.46354	1.0:0.0:0.0:0.0	.	9;9	B4DW30;Q9Y230	.;RUVB2_HUMAN	E	9	ENSP00000221413:K9E	ENSP00000221413:K9E	K	+	1	0	RUVBL2	54194400	1.000000	0.71417	1.000000	0.80357	0.745000	0.42441	7.232000	0.78116	1.873000	0.54277	0.448000	0.29417	AAA			0.547	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000466235.1			
Unknown	0	bcgsc.ca	37	19	50222914	50222914	+	IGR	SNP	G	G	A	rs3810261	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	35	0	0		WXS	Illumina HiSeq	Phase_1	42	0.12	5	.	3	0.33	1		RNA	SNP		37																																																																																					0	0.637										
PDIA6	10130	bcgsc.ca	37	2	10959407	10959407	+	Missense_Mutation	SNP	A	A	C	rs72779451	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:10959407A>C	ENST00000404371.2	-	3	505	c.168T>G	c.(166-168)aaT>aaG	p.N56K	PDIA6_ENST00000381611.4_Missense_Mutation_p.N9K|PDIA6_ENST00000404824.2_Missense_Mutation_p.N52K	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		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_1	96	0.05	5	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:10959461G>T	ENST00000404371.2	-	3	451	c.114C>A	c.(112-114)gcC>gcA	p.A38A	PDIA6_ENST00000381611.4_5'UTR|PDIA6_ENST00000404824.2_Silent_p.A34A	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			Somatic	62	0	0		WXS	Illumina HiSeq	Phase_1	70	0.07	5	.	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	
PDIA6	10130	bcgsc.ca	37	2	10959475	10959475	+	Missense_Mutation	SNP	G	G	C	rs72779453	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:10959475G>C	ENST00000404371.2	-	3	437	c.100C>G	c.(100-102)Cca>Gca	p.P34A	PDIA6_ENST00000381611.4_5'UTR|PDIA6_ENST00000404824.2_Missense_Mutation_p.P30A	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)		GGAGAAGTTGGTGAGCCTGAA	0.483													C|||	427	0.0852636	0.0287	0.1268	5008	,	,		20033	0.0585		0.1879	False		,,,				2504	0.0542				.	GBM(73;509 1219 34219 41343 41551)												.	.			0			.																																									SO:0001583	missense	10130	.			AAGTTGGTGAGCC	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.100C>G	2.37:g.10959475G>C	ENSP00000385385:p.Pro34Ala		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_1	66	0.08	5	.	0		0	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Missense_Mutation	SNP	ENST00000404371.2	37		229	0.10485347985347986	19	0.03861788617886179	36	0.09944751381215469	42	0.07342657342657342	132	0.1741424802110818	C	0.008	-1.915485	0.00503	.	.	ENSG00000143870	ENST00000404371;ENST00000404824	T;T	0.06294	3.77;3.32	0.94	0.94	0.19513	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38045	-0.9679	7	0.87932	D	0	.	4.8419	0.13494	0.0:0.6026:0.3974:0.0	.	30;34	B5MCQ5;Q15084-2	.;.	A	34;30	ENSP00000385385:P34A;ENSP00000384459:P30A	ENSP00000385385:P34A	P	-	1	0	PDIA6	10876926	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.578000	0.05841	-0.019000	0.14055	-0.357000	0.07601	CCA			0.483	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000323575.2		NM_005742	
Unknown	0	bcgsc.ca	37	2	38044830	38044830	+	IGR	SNP	C	C	G	rs4670218	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:38044830C>G								AC006369.3 (70641 upstream) : LINC00211 (8559 downstream)																							GAATTCGAATCCTACAAGGGA	0.383													C|||	1673	0.334065	0.3986	0.3372	5008	,	,		19864	0.3115		0.3022	False		,,,				2504	0.3006				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCGAATCCTACAA																													2.37:g.38044830C>G			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	51	0.10	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.383										
Unknown	0	bcgsc.ca	37	2	43053772	43053772	+	IGR	SNP	C	C	T	rs13013413	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	81	0	0		WXS	Illumina HiSeq	Phase_1	72	0.18	13	.	0		0		RNA	SNP		37																																																																																					0	0.403										
LINC01122	400955	bcgsc.ca	37	2	58688907	58688907	+	lincRNA	SNP	G	G	A	rs2075171	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	214	0.0046728972	1		WXS	Illumina HiSeq	Phase_1	211	0.05	11	.	153	0.00	0		RNA	SNP	ENST00000452840.1	37																																																																																						0.507	AC007092.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000327022.1			
Unknown	0	bcgsc.ca	37	2	65432857	65432857	+	IGR	SNP	T	T	C	rs11887325	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:65432857T>C								SNORA74 (46863 upstream) : ACTR2 (22029 downstream)																							GATCAATTTATCAGAAAGTTT	0.428													-|||	333	0.0664936	0.0582	0.0576	5008	,	,		23005	0.003		0.1839	False		,,,				2504	0.0286				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AATTTATCAGAAA																													2.37:g.65432857T>C			Somatic	271	0	0		WXS	Illumina HiSeq	Phase_1	263	0.05	12	.	446	0.00	0		RNA	SNP		37																																																																																					0	0.428										
Unknown	0	bcgsc.ca	37	2	65432952	65432952	+	IGR	SNP	T	T	C	rs35295972	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:65432952T>C								SNORA74 (46958 upstream) : ACTR2 (21934 downstream)																							AAATATCAGTTGGATCCCACT	0.423													-|||	431	0.0860623	0.1278	0.0663	5008	,	,		22699	0.003		0.1839	False		,,,				2504	0.0286				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCAGTTGGATCC																													2.37:g.65432952T>C			Somatic	267	0	0		WXS	Illumina HiSeq	Phase_1	264	0.04	10	.	547	0.00	0		RNA	SNP		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	2	81421951	81421951	+	IGR	SNP	A	A	G	rs13430688	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	58	0	0		WXS	Illumina HiSeq	Phase_1	55	0.16	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	71	0.15	11	.	0		0		RNA	SNP		37																																																																																					0	0.597										
LOC1720	1720	bcgsc.ca	37	2	83084350	83084350	+	IGR	SNP	A	A	T	rs11126880	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	63	0	0		WXS	Illumina HiSeq	Phase_1	46	0.13	6	.	0		0		RNA	SNP		37																																																																																					0	0.333										
IGKV1D-13	28902	bcgsc.ca	37	2	90193417	90193417	+	RNA	SNP	A	A	G	rs1724244	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	356	0.0028089888	1		WXS	Illumina HiSeq	Phase_1	312	0.04	14	.	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;mdanderson.org	37	2	90229260	90229260	+	RNA	SNP	T	T	C	rs842173	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	137	0	0		WXS	Illumina HiSeq	Phase_1	112	0.07	8	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	197	0.0101522843	2		WXS	Illumina HiSeq	Phase_1	216	0.04	8	.	3	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	
ANKRD20A8P	729171	broad.mit.edu	37	2	95490959	95490960	+	RNA	INS	-	-	TGC	rs540082511|rs372560034	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:95490959_95490960insTGC	ENST00000432432.2	-	0	1194					NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene																		gctgctgttgttgctgctgctg	0.421																																					.													.	.			0			.																																											0	.			CTGTTGTTGCTGC			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95490966_95490968dupTGC			Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	10	0.40	4	.	1	0.00	0	A6NC18	RNA	INS	ENST00000432432.2	37																																																																																						0.421	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene		OTTHUMT00000451404.1			
PPP1R2P5	649489	bcgsc.ca	37	2	107557712	107557712	+	IGR	SNP	G	G	A	rs12993155	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:107557712G>A								ST6GAL2 (54148 upstream) : AC006227.1 (313434 downstream)																							ATCATCACCCGTTATACCATG	0.398													A|||	2145	0.428315	0.2859	0.5216	5008	,	,		21751	0.4831		0.4761	False		,,,				2504	0.4489				.													.	.			0			.																																									SO:0001628	intergenic_variant	649489	.			TCACCCGTTATAC																													2.37:g.107557712G>A			Somatic	37	0	0		WXS	Illumina HiSeq	Phase_1	32	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.398										
ISCA1P6	100130549	bcgsc.ca	37	2	129276720	129276720	+	IGR	SNP	T	T	C	rs841094	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	186	0.0053763441	1		WXS	Illumina HiSeq	Phase_1	221	0.08	17	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.602										
RHOQP3	284988	bcgsc.ca	37	2	130970911	130970911	+	IGR	SNP	A	A	G	rs12471586	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:130970911A>G								TUBA3E (14877 upstream) : AC018804.7 (18016 downstream)																							TGCCCCCCACAGTGACGCTGA	0.582													g|||	2681	0.535343	0.5484	0.5821	5008	,	,		17259	0.5675		0.4712	False		,,,				2504	0.5174				.													.	.			0			.																																									SO:0001628	intergenic_variant	284988	.			CCCCACAGTGACG																													2.37:g.130970911A>G			Somatic	154	0.012987013	2		WXS	Illumina HiSeq	Phase_1	162	0.10	17	.	0		0		RNA	SNP		37																																																																																					0	0.582										
AC018804.7	0	bcgsc.ca	37	2	130987792	130987792	+	RNA	SNP	G	G	A	rs12992461	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:130987792G>A	ENST00000450578.1	+	0	0																											GCACATCAGCGTGCTGGTGCC	0.607													.|||	1404	0.280351	0.0991	0.4395	5008	,	,		21341	0.2024		0.3877	False		,,,				2504	0.3824				.													.	.			0			.																																											0	.			ATCAGCGTGCTGG																													2.37:g.130987792G>A			Somatic	80	0.0125	1		WXS	Illumina HiSeq	Phase_1	95	0.06	6	.	14	0.00	0		RNA	SNP	ENST00000450578.1	37																																																																																						0.607	AC018804.7-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000332326.2			
GNAQP1	2777	bcgsc.ca	37	2	132181483	132181483	+	IGR	SNP	G	G	T	rs1059524	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:132181483G>T								AC073869.19 (14861 upstream) : RP11-109E12.1 (37910 downstream)																							TAGATAATTTGGTCACTGGGT	0.502													t|||	1883	0.375998	0.1687	0.5159	5008	,	,		19202	0.754		0.2266	False		,,,				2504	0.3211				.													.	.			0			.																																									SO:0001628	intergenic_variant	2777	.			TAATTTGGTCACT																													2.37:g.132181483G>T			Somatic	66	0	0		WXS	Illumina HiSeq	Phase_1	65	0.09	6	.	2	1.00	2		RNA	SNP		37																																																																																					0	0.502										
GNAQP1	2777	bcgsc.ca	37	2	132182138	132182138	+	IGR	SNP	G	G	T	rs3730150	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:132182138G>T								AC073869.19 (15516 upstream) : RP11-109E12.1 (37255 downstream)																							GCTCATACTTGTATGGGATCT	0.443													g|||	1824	0.364217	0.1354	0.5101	5008	,	,		22068	0.749		0.2276	False		,,,				2504	0.3139				.													.	.			0			.																																									SO:0001628	intergenic_variant	2777	.			ATACTTGTATGGG																													2.37:g.132182138G>T			Somatic	76	0	0		WXS	Illumina HiSeq	Phase_1	77	0.08	6	.	11	0.00	0		RNA	SNP		37																																																																																					0	0.443										
GNAQP1	2777	bcgsc.ca	37	2	132182159	132182159	+	IGR	SNP	T	T	C	rs3730148	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:132182159T>C								AC073869.19 (15537 upstream) : RP11-109E12.1 (37234 downstream)																							TGAGTGAGTCTATGGCTCTGA	0.463													c|||	1826	0.364617	0.1339	0.5086	5008	,	,		21153	0.754		0.2276	False		,,,				2504	0.3139				.													.	.			0			.																																									SO:0001628	intergenic_variant	2777	.			TGAGTCTATGGCT																													2.37:g.132182159T>C			Somatic	75	0	0		WXS	Illumina HiSeq	Phase_1	78	0.08	6	.	44	0.93	41		RNA	SNP		37																																																																																					0	0.463										
MZT2A	653784	broad.mit.edu	37	2	132250656	132250656	+	5'Flank	SNP	C	C	G	rs2272360	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:132250656C>G	ENST00000309451.6	-	0	0				MZT2A_ENST00000410036.2_5'Flank|AC093838.4_ENST00000438378.2_RNA|MIR4784_ENST00000579560.1_RNA	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						GACGTTTTGGCGCGGTGGCGG	0.677													.|||	1677	0.334864	0.1346	0.4251	5008	,	,		13603	0.6806		0.2197	False		,,,				2504	0.3037				.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			TTTTGGCGCGGTG	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606		2.37:g.132250656C>G	Exception_encountered		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	21	0.24	5	.	7	0.00	0	Q3SWV8|Q8WVB2	RNA	SNP	ENST00000309451.6	37	CCDS42758.1																																																																																					0.677	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000331811.2			
LOC150776	150776	bcgsc.ca	37	2	132257830	132257830	+	RNA	SNP	C	C	T	rs13035779	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	197	0.0050761421	1		WXS	Illumina HiSeq	Phase_1	172	0.06	11	.	47	0.00	0		RNA	SNP	ENST00000438378.2	37																																																																																						0.567	AC093838.4-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331819.7			
ZNF806	646915	bcgsc.ca	37	2	133075301	133075301	+	IGR	SNP	A	A	G	rs17394868	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:133075301A>G								AC097532.2 (23351 upstream) : RP11-725P16.2 (27887 downstream)																							GCACTCATCTAGGAGAAAAAT	0.418													.|||	372	0.0742812	0.0393	0.049	5008	,	,		20648	0.125		0.0944	False		,,,				2504	0.0665				.													.	.			0			.																																									SO:0001628	intergenic_variant	646915	.			TCATCTAGGAGAA																													2.37:g.133075301A>G			Somatic	121	0	0		WXS	Illumina HiSeq	Phase_1	126	0.07	9	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.418										
YWHAEP5	440917	bcgsc.ca	37	2	139045855	139045855	+	IGR	SNP	C	C	T	rs35998722	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	87	0	0		WXS	Illumina HiSeq	Phase_1	129	0.09	11	.	4	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	126	0	0		WXS	Illumina HiSeq	Phase_1	141	0.06	8	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.423										
Unknown	0	bcgsc.ca	37	2	139065003	139065003	+	IGR	SNP	G	G	C	rs7570952	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:139065003G>C								AC069394.1 (201528 upstream) : AC097721.2 (110850 downstream)																							CATTGAGAAAGGGTTATTGCA	0.388													G|||	1888	0.376997	0.4138	0.3847	5008	,	,		21685	0.5288		0.2555	False		,,,				2504	0.2904				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGAAAGGGTTAT																													2.37:g.139065003G>C			Somatic	95	0	0		WXS	Illumina HiSeq	Phase_1	78	0.15	12	.	0		0		RNA	SNP		37																																																																																					0	0.388										
LOC101927641	101927641	bcgsc.ca	37	2	200525076	200525076	+	lincRNA	SNP	A	A	G	rs77443884	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	70	0	0		WXS	Illumina HiSeq	Phase_1	69	0.09	6	.	0		0		RNA	SNP	ENST00000439734.1	37																																																																																						0.587	AC093590.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000335491.2			
CRYGB	1419	bcgsc.ca	37	2	209010891	209010891	+	5'UTR	SNP	G	G	A	rs2289917	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	116	0.0086206897	1		WXS	Illumina HiSeq	Phase_1	118	0.11	13	.	1	0.00	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	
MFF	56947	hgsc.bcm.edu	37	2	228194321	228194321	+	Splice_Site	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:228194321G>T	ENST00000353339.3	+	3	301		c.e3-1		MFF_ENST00000476924.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000392059.1_Splice_Site|MFF_ENST00000409565.1_Intron|MFF_ENST00000349901.7_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000409616.1_Splice_Site	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor						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						CTTTTTTACAGCTGGAAAAGC	0.313																																					.													.	.			0			.																																									SO:0001630	splice_region_variant	56947	.			TTTACAGCTGGAA	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	ENST00000353339.3:c.-140-1G>T	2.37:g.228194321G>T			Somatic	109	0	0		WXS	Illumina HiSeq	.	129	0.06	8	.	4	0.00	0	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Splice_Site	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																					0.313	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000256887.2		NM_020194	Intron
MFF	56947	bcgsc.ca	37	2	228194480	228194481	+	Missense_Mutation	DNP	AG	AG	TT	rs3211098|rs3211097|rs386655869	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr2:228194480_228194481AG>TT	ENST00000353339.3	+	3	460_461	c.19_20AG>TT	c.(19-21)AGt>TTt	p.S7F	MFF_ENST00000476924.1_Intron|MFF_ENST00000354503.6_Intron|MFF_ENST00000392059.1_Missense_Mutation_p.S7F|MFF_ENST00000409565.1_Intron|MFF_ENST00000349901.7_Intron|MFF_ENST00000337110.7_Intron|MFF_ENST00000304593.9_Intron|MFF_ENST00000524634.1_Intron|MFF_ENST00000409616.1_5'UTR	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		Somatic	285	0.0070175439	2		WXS	Illumina HiSeq	Phase_1	339	0.09	29	NM_020194	28	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	
CROCC2	728763	bcgsc.ca	37	2	241865211	241865211	+	Missense_Mutation	SNP	G	G	A	rs56199645	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	165	0.0060606061	1		WXS	Illumina HiSeq	Phase_1	149	0.06	9	.	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					
Unknown	0	bcgsc.ca	37	20	6194421	6194421	+	IGR	SNP	A	A	C	rs6076962	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:6194421A>C								FERMT1 (90230 upstream) : AL109618.1 (15019 downstream)																							CCATTCAGAAAATTTTCAGAC	0.388													A|||	2180	0.435304	0.5197	0.4135	5008	,	,		20458	0.253		0.5835	False		,,,				2504	0.3722				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCAGAAAATTTTC																													20.37:g.6194421A>C			Somatic	91	0	0		WXS	Illumina HiSeq	Phase_1	96	0.14	13	.	17	0.00	0		RNA	SNP		37																																																																																					0	0.388										
SDAD1P2	400836	bcgsc.ca	37	20	10366898	10366898	+	IGR	SNP	T	T	C	rs2223654	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:10366898T>C								SNAP25-AS1 (17474 upstream) : MKKS (14758 downstream)																							TAAGCTTCTGTGAAAGACTTT	0.343													C|||	3702	0.739217	0.8684	0.8501	5008	,	,		21665	0.5288		0.7634	False		,,,				2504	0.6779				.													.	.			0			.																																									SO:0001628	intergenic_variant	400836	.			CTTCTGTGAAAGA																													20.37:g.10366898T>C			Somatic	43	0	0		WXS	Illumina HiSeq	Phase_1	32	0.22	7	.	31	0.00	0		RNA	SNP		37																																																																																					0	0.343										
SDAD1P2	400836	bcgsc.ca	37	20	10367323	10367323	+	IGR	SNP	C	C	G	rs6039900	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:10367323C>G								SNAP25-AS1 (17899 upstream) : MKKS (14333 downstream)																							CTTGAGTGAACTAAGGAGAAG	0.363													G|||	3462	0.691294	0.6974	0.8444	5008	,	,		20695	0.5268		0.7614	False		,,,				2504	0.6718				.													.	.			0			.																																									SO:0001628	intergenic_variant	400836	.			AGTGAACTAAGGA																													20.37:g.10367323C>G			Somatic	18	0	0		WXS	Illumina HiSeq	Phase_1	25	0.28	7	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.363										
SDAD1P2	400836	bcgsc.ca	37	20	10367909	10367909	+	IGR	SNP	A	A	C	rs6108519	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:10367909A>C								SNAP25-AS1 (18485 upstream) : MKKS (13747 downstream)																							TACCAGTCTCAGTGAGGAGCA	0.428													A|||	2897	0.578474	0.5915	0.7954	5008	,	,		21614	0.3532		0.7097	False		,,,				2504	0.5041				.													.	.			0			.																																									SO:0001628	intergenic_variant	400836	.			AGTCTCAGTGAGG																													20.37:g.10367909A>C			Somatic	209	0.004784689	1		WXS	Illumina HiSeq	Phase_1	186	0.13	24	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.428										
FRG1B	284802	bcgsc.ca	37	20	29628233	29628233	+	Missense_Mutation	SNP	A	A	G			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:29628233A>G	ENST00000278882.3	+	6	615	c.235A>G	c.(235-237)Atg>Gtg	p.M79V	FRG1B_ENST00000439954.2_Missense_Mutation_p.M84V|FRG1B_ENST00000358464.4_Missense_Mutation_p.M79V			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	79										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTAGGGGAAAATGGCTTTGTT	0.363																																					.													.	FRG1B	181		0			.																																									SO:0001583	missense	284802	.			GGGAAAATGGCTT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.235A>G	20.37:g.29628233A>G	ENSP00000278882:p.Met79Val		Somatic	536	0.0186567164	10		WXS	Illumina HiSeq	Phase_1	475	0.03	14	.	277	0.00	0	C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	a	3.138	-0.176853	0.06380	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.41065	1.01	2.08	2.08	0.27032	Actin cross-linking (1);	0.040228	0.85682	D	0.000000	T	0.23370	0.0565	.	.	.	0.41063	D	0.985397	B;B	0.17852	0.002;0.024	B;B	0.25140	0.03;0.058	T	0.04593	-1.0940	9	0.11794	T	0.64	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	84;79	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	V	79;84;79	ENSP00000408863:M84V	ENSP00000278882:M79V	M	+	1	0	FRG1B	28241894	1.000000	0.71417	1.000000	0.80357	0.277000	0.26821	4.813000	0.62620	1.208000	0.43306	0.347000	0.21830	ATG			0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000078494.2		NR_003579	
Unknown	0	bcgsc.ca	37	20	31635384	31635384	+	IGR	SNP	G	G	A	rs743172	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr20:31635384G>A								BPIFB6 (3531 upstream) : BPIFB3 (7845 downstream)																							ACTCAGCAACGGGGAGGCCTT	0.592													A|||	3282	0.655351	0.8011	0.5288	5008	,	,		19711	0.7788		0.4771	False		,,,				2504	0.6043				.													.	.			0			.																																									SO:0001628	intergenic_variant	391242	.			AGCAACGGGGAGG																													20.37:g.31635384G>A			Somatic	36	0	0		WXS	Illumina HiSeq	Phase_1	24	0.21	5	.	0		0		RNA	SNP		37																																																																																					0	0.592										
BAGE2	85319	broad.mit.edu	37	21	11058613	11058614	+	RNA	INS	-	-	A	rs60445243|rs377480117	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:11058613_11058614insA	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GATTTTTTTTTAAAGCAAATAG	0.248																																					.													.	.			0			.																																											85319	.			TTTTTTTAAAGCA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058616_11058616dupA			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0	A8K925|Q08ER0	RNA	INS	ENST00000470054.1	37																																																																																						0.248	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000157417.3		NM_182482	
ANKRD30BP1	642460	bcgsc.ca	37	21	14795475	14795475	+	IGR	SNP	G	G	A	rs459504	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:14795475G>A								MIR3156-3 (16694 upstream) : AP001465.5 (122878 downstream)																							GTTCTTCATCGTCCTATTGCT	0.303													.|||	665	0.132788	0.0189	0.3847	5008	,	,		16410	0.001		0.2803	False		,,,				2504	0.092				.													.	.			0			.																																									SO:0001628	intergenic_variant	642460	.			TTCATCGTCCTAT																													21.37:g.14795475G>A			Somatic	114	0	0		WXS	Illumina HiSeq	Phase_1	126	0.07	9	.	0		0		RNA	SNP		37																																																																																					0	0.303										
SNX19P1	378810	bcgsc.ca	37	21	14899553	14899553	+	IGR	SNP	A	A	G	rs2257395	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:14899553A>G								MIR3156-3 (120772 upstream) : AP001465.5 (18800 downstream)																							ATTACAGCCCAAGAGCTCAGT	0.532													G|||	3269	0.652756	0.7428	0.4207	5008	,	,		20339	0.9028		0.5586	False		,,,				2504	0.5348				.													.	.			0			.																																									SO:0001628	intergenic_variant	378810	.			CAGCCCAAGAGCT																													21.37:g.14899553A>G			Somatic	22	0	0		WXS	Illumina HiSeq	Phase_1	28	0.25	7	.	0		0		RNA	SNP		37																																																																																					0	0.532										
PPP6R2P1	100631381	bcgsc.ca	37	21	15384535	15384535	+	IGR	SNP	G	G	C	rs1297100	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:15384535G>C								AP001634.1 (26695 upstream) : AP001347.6 (15206 downstream)																							AGACCATGATGCGCCTGGGGC	0.632													.|||	1334	0.266374	0.1573	0.3199	5008	,	,		17912	0.25		0.4354	False		,,,				2504	0.2188				.													.	.			0			.																																									SO:0001628	intergenic_variant	100631381	.			CATGATGCGCCTG																													21.37:g.15384535G>C			Somatic	28	0	0		WXS	Illumina HiSeq	Phase_1	26	0.15	4	.	0		0		RNA	SNP		37																																																																																					0	0.632										
ANKRD20A18P	391269	bcgsc.ca	37	21	15436681	15436681	+	RNA	SNP	G	G	C	rs11908695	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:15436681G>C	ENST00000428809.1	+	0	177				AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000448463.1_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			Somatic	187	0.0053475936	1		WXS	Illumina HiSeq	Phase_1	257	0.13	33	.	2	0.00	0		RNA	SNP	ENST00000428809.1	37																																																																																						0.607	AP001347.6-001	KNOWN	basic	antisense	antisense		OTTHUMT00000157812.1			
AP001347.6	0	broad.mit.edu	37	21	15461077	15461078	+	RNA	INS	-	-	A	rs200906842		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:15461077_15461078insA	ENST00000428809.1	+	0	372				AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000448463.1_RNA																							CTTAGCTACTTaaaaaaagaaa	0.342																																					.													.	.			0			.																																											0	.			GCTACTTAAAAAA																													21.37:g.15461084_15461084dupA			Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	INS	ENST00000428809.1	37																																																																																						0.342	AP001347.6-001	KNOWN	basic	antisense	antisense		OTTHUMT00000157812.1			
SLC6A6P1	54019	bcgsc.ca	37	21	20617291	20617291	+	IGR	SNP	G	G	T	rs9980261	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	44	0	0		WXS	Illumina HiSeq	Phase_1	42	0.14	6	.	0		0		RNA	SNP		37																																																																																					0	0.587										
THUMPD1P1	391276	bcgsc.ca	37	21	30275638	30275638	+	IGR	SNP	C	C	T	rs2248470	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	45	0	0		WXS	Illumina HiSeq	Phase_1	83	0.08	7	.	0		0		RNA	SNP		37																																																																																					0	0.438										
UBE3AP2	7339	bcgsc.ca	37	21	32434300	32434300	+	IGR	SNP	T	T	C	rs1888445	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:32434300T>C								KRTAP19-8 (23505 upstream) : TIAM1 (56433 downstream)																							ATTCAACTGCTGTCCTTGAAC	0.393													T|||	1761	0.351637	0.1626	0.3487	5008	,	,		18392	0.2202		0.5736	False		,,,				2504	0.5164				.													.	.			0			.																																									SO:0001628	intergenic_variant	7339	.			AACTGCTGTCCTT																													21.37:g.32434300T>C			Somatic	60	0	0		WXS	Illumina HiSeq	Phase_1	105	0.10	10	.	0		0		RNA	SNP		37																																																																																					0	0.393										
UBE3AP2	7339	bcgsc.ca	37	21	32435334	32435334	+	IGR	SNP	T	T	C	rs11088156	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:32435334T>C								KRTAP19-8 (24539 upstream) : TIAM1 (55399 downstream)																							CTTGGTGTGTTGTTTAGCTTT	0.398													T|||	1763	0.352037	0.1649	0.3473	5008	,	,		18847	0.2202		0.5726	False		,,,				2504	0.5174				.													.	.			0			.																																									SO:0001628	intergenic_variant	7339	.			GTGTGTTGTTTAG																													21.37:g.32435334T>C			Somatic	41	0	0		WXS	Illumina HiSeq	Phase_1	42	0.19	8	.	0		0		RNA	SNP		37																																																																																					0	0.398										
TIAM1	7074	bcgsc.ca	37	21	32638549	32638550	+	Missense_Mutation	DNP	CC	CC	AT	rs2070418|rs386817934|rs2070417	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:32638549_32638550CC>AT	ENST00000286827.3	-	5	1210_1211	c.739_740GG>AT	c.(739-741)GGg>ATg	p.G247M	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.G247M	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		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_1	193	0.05	9	NM_003253	152	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	
ITSN1	6453	hgsc.bcm.edu;bcgsc.ca	37	21	35144472	35144491	+	Frame_Shift_Del	DEL	GCCCAGCTGGAGCGGGCGGA	GCCCAGCTGGAGCGGGCGGA	-	rs375451100|rs200196886|rs544261869|rs148618330|rs143580796		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GCCCAGCTGGAGCGGGCGGA	GCCCAGCTGGAGCGGGCGGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:35144472_35144491delGCCCAGCTGGAGCGGGCGGA	ENST00000381318.3	+	12	1438_1457	c.1150_1169delGCCCAGCTGGAGCGGGCGGA	c.(1150-1170)gcccagctggagcgggcggagfs	p.AQLERAE384fs	ITSN1_ENST00000399353.1_Frame_Shift_Del_p.AQLERAE347fs|ITSN1_ENST00000399338.4_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000399349.1_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000488166.1_3'UTR|ITSN1_ENST00000399367.3_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000379960.5_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000399352.1_Frame_Shift_Del_p.AQLERAE384fs|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000437442.2_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000399355.2_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000381285.4_Frame_Shift_Del_p.AQLERAE384fs|ITSN1_ENST00000399326.3_Frame_Shift_Del_p.AQLERAE384fs	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	384	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GGAGCGCCTGGCCCAGCTGGAGCGGGCGGAGCAGGAGAGG	0.582																																					p.383_390del													.	ITSN1	166		0			c.1149_1168del																																									SO:0001589	frameshift_variant	6453	exon12			CGCCTGGCCCAGC	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1150_1169delGCCCAGCTGGAGCGGGCGGA	21.37:g.35144472_35144491delGCCCAGCTGGAGCGGGCGGA	ENSP00000370719:p.Ala384fs		Somatic	124	0	0		WXS	Illumina HiSeq	.	150	0.12	18	NM_001001132	62	0.00	0	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Frame_Shift_Del	DEL	ENST00000381318.3	37	CCDS33545.1																																																																																					0.582	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000140070.4		NM_003024	
ITSN1	6453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	35147283	35147283	+	Missense_Mutation	SNP	G	G	C			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr21:35147283G>C	ENST00000381318.3	+	14	1755	c.1467G>C	c.(1465-1467)aaG>aaC	p.K489N	ITSN1_ENST00000399353.1_Missense_Mutation_p.K452N|ITSN1_ENST00000399338.4_Missense_Mutation_p.K489N|ITSN1_ENST00000399349.1_Missense_Mutation_p.K489N|ITSN1_ENST00000399367.3_Missense_Mutation_p.K489N|ITSN1_ENST00000379960.5_Missense_Mutation_p.K489N|ITSN1_ENST00000399352.1_Missense_Mutation_p.K489N|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Missense_Mutation_p.K489N|ITSN1_ENST00000437442.2_Missense_Mutation_p.K489N|ITSN1_ENST00000399355.2_Missense_Mutation_p.K489N|ITSN1_ENST00000381285.4_Missense_Mutation_p.K489N|ITSN1_ENST00000399326.3_Missense_Mutation_p.K489N	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	489	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						ATGATAAAAAGCATCAACTAG	0.323																																					p.K489N													.	.			0			c.G1467C												72.0	74.0	73.0					21																	35147283		2203	4300	6503	SO:0001583	missense	6453	exon14			TAAAAAGCATCAA	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1467G>C	21.37:g.35147283G>C	ENSP00000370719:p.Lys489Asn		Somatic	164	0	0		WXS	Illumina HiSeq	.	183	0.20	37	NM_001001132	46	0.11	5	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.914926	0.52546	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.46451	1.54;0.87;0.93;0.87;1.54;1.54;0.92;1.54;1.54;1.54;1.54;0.92	5.07	1.75	0.24633	.	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	N	0.22421	0.69	0.45662	D	0.998585	D;D;B;D;D;P;D;D;D;D	0.89917	1.0;0.999;0.319;0.992;0.993;0.799;0.987;0.987;0.989;0.999	D;D;B;P;P;B;P;P;P;D	0.71656	0.974;0.962;0.149;0.776;0.805;0.343;0.776;0.776;0.885;0.962	T	0.27706	-1.0066	10	0.48119	T	0.1	.	8.9299	0.35663	0.3722:0.0:0.6278:0.0	.	452;452;452;489;489;489;489;489;489;452	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	N	452;489;489;489;489;489;489;489;489;489;489;489;489;489	ENSP00000382290:K452N;ENSP00000370719:K489N;ENSP00000370691:K489N;ENSP00000370685:K489N;ENSP00000382301:K489N;ENSP00000382289:K489N;ENSP00000382292:K489N;ENSP00000382286:K489N;ENSP00000382275:K489N;ENSP00000387377:K489N;ENSP00000382265:K489N;ENSP00000369294:K489N	ENSP00000369294:K489N	K	+	3	2	ITSN1	34069153	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.924000	0.28777	0.535000	0.28714	0.591000	0.81541	AAG			0.323	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000140070.4		NM_003024	
OR11H1	81061	bcgsc.ca;mdanderson.org	37	22	16449050	16449050	+	Missense_Mutation	SNP	G	G	A	rs78350717	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:16449050G>A	ENST00000252835.4	-	1	755	c.755C>T	c.(754-756)gCc>gTc	p.A252V		NM_001005239.1	NP_001005239.1	Q8NG94	O11H1_HUMAN	olfactory receptor, family 11, subfamily H, member 1	252						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(2)|large_intestine(3)|lung(4)|skin(1)	11	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.208)		Kidney(3;0.00216)|KIRC - Kidney renal clear cell carcinoma(3;0.00244)|Lung(27;0.0724)|COAD - Colon adenocarcinoma(3;0.211)		GGTAGAGAAGGCCTTATGTCT	0.438													G|||	1036	0.206869	0.0703	0.1931	5008	,	,		22319	0.25		0.3608	False		,,,				2504	0.1984				p.A252V													.	OR11H1	44		0			c.C755T							G	VAL/ALA	489,3913	225.9+/-241.6	32,425,1744	117.0	114.0	115.0		755	1.7	1.0	22	dbSNP_134	115	3111,5483	469.5+/-367.6	551,2009,1737	no	missense	OR11H1	NM_001005239.1	64	583,2434,3481	AA,AG,GG		36.1997,11.1086,27.7008	probably-damaging	252/327	16449050	3600,9396	2201	4297	6498	SO:0001583	missense	81061	exon1			GAGAAGGCCTTAT	AP000535, AF399611	CCDS74807.1	22q11.1	2012-08-09			ENSG00000130538	ENSG00000130538		"""GPCR / Class A : Olfactory receptors"""	15404	protein-coding gene	gene with protein product						12213199	Standard	NM_001005239		Approved	OR22-1	uc011agd.2	Q8NG94	OTTHUMG00000030069	ENST00000252835.4:c.755C>T	22.37:g.16449050G>A	ENSP00000252835:p.Ala252Val		Somatic	337	0	0		WXS	Illumina HiSeq	Phase_1	309	0.07	21	NM_001005239	0		0	Q6IEX0|Q96R32	Missense_Mutation	SNP	ENST00000252835.4	37	CCDS33594.1	.	.	.	.	.	.	.	.	.	.	g	13.53	2.265663	0.40095	0.111086	0.361997	ENSG00000130538	ENST00000252835	T	0.00342	8.03	1.73	1.73	0.24493	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000857	T	0.00012	0.0000	M	0.84433	2.695	0.48185	P	3.9999999999995595E-4	D	0.71674	0.998	D	0.71184	0.972	T	0.48990	-0.8985	9	0.62326	D	0.03	.	9.578	0.39470	0.0:0.0:1.0:0.0	.	252	Q8NG94	O11H1_HUMAN	V	252	ENSP00000252835:A252V	ENSP00000252835:A252V	A	-	2	0	OR11H1	14829050	0.963000	0.33076	0.985000	0.45067	0.717000	0.41224	1.891000	0.39738	0.917000	0.36895	0.368000	0.22195	GCC			0.438	OR11H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000074923.2		NM_001005239	
CLDN5	7122	mdanderson.org	37	22	19511442	19511442	+	Missense_Mutation	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:19511442C>T	ENST00000406028.1	-	2	1652	c.592G>A	c.(592-594)Gcc>Acc	p.A198T	CLDN5_ENST00000403084.1_Missense_Mutation_p.A198T|CLDN5_ENST00000413119.2_Missense_Mutation_p.A198T			O00501	CLD5_HUMAN	claudin 5	113					calcium-independent cell-cell adhesion (GO:0016338)|myelination (GO:0042552)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			liver(1)|lung(2)|prostate(1)	4	Colorectal(54;0.0993)					CGCGCCTTGGCCGGGCCCGGG	0.716																																					p.A198T													.	.			0			c.G592A												8.0	9.0	9.0					22																	19511442		2158	4249	6407	SO:0001583	missense	7122	exon1			CCTTGGCCGGGCC	AF000959	CCDS13763.2	22q11.21	2008-08-01	2008-08-01		ENSG00000184113	ENSG00000184113		"""Claudins"""	2047	protein-coding gene	gene with protein product		602101	"""transmembrane protein deleted in velocardiofacial syndrome"""	AWAL, TMVCF		9441748, 9192844	Standard	NM_003277		Approved	CPETRL1, BEC1	uc002zpu.2	O00501	OTTHUMG00000150441	ENST00000406028.1:c.592G>A	22.37:g.19511442C>T	ENSP00000385477:p.Ala198Thr		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	30	0.17	5	NM_001130861	10	0.00	0	B3KS11|Q53XW2|Q8WUW3	Missense_Mutation	SNP	ENST00000406028.1	37	CCDS13763.2	.	.	.	.	.	.	.	.	.	.	C	11.09	1.535573	0.27475	.	.	ENSG00000184113	ENST00000406028;ENST00000403084;ENST00000413119	D;D;D	0.88664	-2.41;-2.41;-2.41	4.89	2.8	0.32819	.	0.785759	0.11798	N	0.528455	T	0.81049	0.4742	N	0.26092	0.79	0.09310	N	1	B	0.24186	0.099	B	0.25405	0.06	T	0.67432	-0.5672	10	0.34782	T	0.22	.	7.9783	0.30168	0.0:0.7166:0.0:0.2834	.	198	D3DX19	.	T	198	ENSP00000385477:A198T;ENSP00000384554:A198T;ENSP00000400612:A198T	ENSP00000384554:A198T	A	-	1	0	CLDN5	17891442	0.000000	0.05858	0.000000	0.03702	0.269000	0.26545	-0.338000	0.07842	0.488000	0.27723	0.462000	0.41574	GCC			0.716	CLDN5-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318122.3		NM_003277	
RIMBP3	85376	bcgsc.ca	37	22	20457060	20457060	+	Silent	SNP	C	C	G	rs200551182		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:20457060C>G	ENST00000426804.1	-	1	4726	c.4242G>C	c.(4240-4242)gtG>gtC	p.V1414V	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	1414										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)			ACCCTCTCTTCACCCCCAGAG	0.637																																					p.V1414V													.	RIMBP3	42		0			c.G4242C																																									SO:0001819	synonymous_variant	85376	exon1			TCTCTTCACCCCC	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.4242G>C	22.37:g.20457060C>G			Somatic	239	0.0041841004	1		WXS	Illumina HiSeq	Phase_1	307	0.08	25	NM_015672	5	0.00	0	Q8IYP7|Q9BY94|Q9UFQ5	Silent	SNP	ENST00000426804.1	37	CCDS46665.1																																																																																					0.637	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318945.2		NM_015672	
RIMBP3	85376	bcgsc.ca;mdanderson.org	37	22	20457204	20457204	+	Silent	SNP	G	G	A	rs141165655		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:20457204G>A	ENST00000426804.1	-	1	4582	c.4098C>T	c.(4096-4098)ggC>ggT	p.G1366G	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	1366										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)			GTTGGCTGGCGCCCAGCTGGG	0.567																																					p.G1366G													.	RIMBP3	42		0			c.C4098T												4.0	4.0	4.0					22																	20457204		991	2754	3745	SO:0001819	synonymous_variant	85376	exon1			GCTGGCGCCCAGC	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.4098C>T	22.37:g.20457204G>A			Somatic	289	0.0034602076	1		WXS	Illumina HiSeq	Phase_1	375	0.06	23	NM_015672	5	0.00	0	Q8IYP7|Q9BY94|Q9UFQ5	Silent	SNP	ENST00000426804.1	37	CCDS46665.1																																																																																					0.567	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318945.2		NM_015672	
RIMBP3	85376	bcgsc.ca	37	22	20457841	20457841	+	Missense_Mutation	SNP	T	T	C	rs202034782	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	783	0	0		WXS	Illumina HiSeq	Phase_1	837	0.04	30	NM_015672	1	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	bcgsc.ca	37	22	21400282	21400282	+	Missense_Mutation	SNP	G	G	C	rs12170538	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:21400282G>C	ENST00000342608.4	+	1	34	c.7G>C	c.(7-9)Ggt>Cgt	p.G3R	AC002472.11_ENST00000450652.1_RNA|AC002472.13_ENST00000543388.1_Missense_Mutation_p.G3R|P2RX6P_ENST00000439119.1_RNA|AC002472.13_ENST00000497328.1_3'UTR																lung(2)	2						AACCATGAGGGGTTCCTGTGA	0.647													g|||	228	0.0455272	0.0726	0.0476	5008	,	,		15796	0.0		0.0885	False		,,,				2504	0.0102				.													.	.			0			.																																									SO:0001583	missense	0	.			ATGAGGGGTTCCT																												ENST00000342608.4:c.7G>C	22.37:g.21400282G>C	ENSP00000341179:p.Gly3Arg		Somatic	115	0.0086956522	1		WXS	Illumina HiSeq	Phase_1	174	0.04	7	.	0		0		Missense_Mutation	SNP	ENST00000342608.4	37		119	0.05448717948717949	39	0.07926829268292683	14	0.03867403314917127	0	0.0	66	0.0870712401055409	G	14.25	2.478578	0.44044	.	.	ENSG00000187905	ENST00000342608;ENST00000543388;ENST00000442047	T;T;T	0.26660	2.03;1.72;2.1	2.49	0.313	0.15842	.	.	.	.	.	T	0.00845	0.0028	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.15492	-1.0435	6	0.72032	D	0.01	.	4.6644	0.12659	0.327:0.0:0.673:0.0	rs12170538;rs52813498;rs12170538	.	.	.	R	3	ENSP00000341179:G3R;ENSP00000441009:G3R;ENSP00000394078:G3R	ENSP00000341179:G3R	G	+	1	0	AC002472.13	19730282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.070000	0.14573	0.134000	0.18681	-0.350000	0.07774	GGT			0.647	AC002472.13-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
LRRC74B	400891	bcgsc.ca;mdanderson.org	37	22	21407656	21407656	+	Missense_Mutation	SNP	T	T	C	rs59837066	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_1	149	0.06	9	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	205	0.05	10	.	26	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;mdanderson.org	37	22	22516998	22516998	+	RNA	SNP	C	C	T	rs2073453	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	122	0	0		WXS	Illumina HiSeq	Phase_1	130	0.08	10	.	15	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;mdanderson.org	37	22	22556270	22556270	+	RNA	SNP	T	T	C	rs5995639	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:22556270T>C	ENST00000390286.2	+	0	96									immunoglobulin lambda variable 11-55 (non-functional)																		AGCCGCCCTCTCTGTCTGCAT	0.612											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	,	,		19000	0.3641		0.493	False		,,,				2504	0.6564				.													.	.			0			.							C		2837,1321		979,879,221	33.0	38.0	36.0			-2.0	0.0	22	dbSNP_114	36	4119,4307		1003,2113,1097	no	intergenic				1982,2992,1318	CC,CT,TT		48.8844,31.7701,44.7235			22556270	6956,5628	2079	4213	6292			28770	.			GCCCTCTCTGTCT	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.22556270T>C			Somatic	62	0	0	757	WXS	Illumina HiSeq	Phase_1	57	0.11	6	.	0		0		RNA	SNP	ENST00000390286.2	37																																																																																						0.612	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	304	0.0032894737	1		WXS	Illumina HiSeq	Phase_1	382	0.07	28	.	0		0		RNA	SNP		37																																																																																					0	0.652										
IGLV7-46	28775	bcgsc.ca;mdanderson.org	37	22	22724341	22724341	+	RNA	SNP	A	A	C	rs9607803	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:22724341A>C	ENST00000390295.2	+	0	271									immunoglobulin lambda variable 7-46 (gene/pseudogene)																		ACTCCTGGACACCTGCCCGGT	0.562													a|||	2135	0.426318	0.3056	0.4957	5008	,	,		16805	0.377		0.4851	False		,,,				2504	0.5307				.													.	.			0			.							T		1104,2684		180,744,970	45.0	46.0	46.0			-7.2	0.0	22	dbSNP_119	46	3840,4372		919,2002,1185	no	intergenic				1099,2746,2155	CC,CA,AA		46.7608,29.1447,41.2			22724341	4944,7056	1894	4106	6000			28775	.			CTGGACACCTGCC	Z73674		22q11.2	2012-02-08	2008-09-12		ENSG00000211649	ENSG00000211649		"""Immunoglobulins / IGL locus"""	5930	other	immunoglobulin gene			"""immunoglobulin lambda variable 7-46"""				Standard	NG_000002		Approved				OTTHUMG00000151040		22.37:g.22724341A>C			Somatic	94	0	0		WXS	Illumina HiSeq	Phase_1	101	0.10	10	.	62	0.00	0		RNA	SNP	ENST00000390295.2	37																																																																																						0.562	IGLV7-46-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000321099.1		NG_000002	
IGLV2-34	28810	bcgsc.ca	37	22	22922640	22922640	+	IGR	SNP	C	C	G	rs464317	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:22922640C>G								LL22NC03-63E9.3 (13633 upstream) : IGLV2-33 (7985 downstream)																							TATGATGTCGCTAATTGGCCC	0.572													G|||	3911	0.78095	0.7753	0.8415	5008	,	,		16096	0.7907		0.7465	False		,,,				2504	0.771				.													.	.			0			.																																									SO:0001628	intergenic_variant	28810	.			ATGTCGCTAATTG																													22.37:g.22922640C>G			Somatic	42	0	0		WXS	Illumina HiSeq	Phase_1	52	0.12	6	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.572										
ARL5AP4	641379	bcgsc.ca	37	22	25082586	25082586	+	IGR	SNP	T	T	G	rs5751933	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:25082586T>G								GGT1 (57614 upstream) : PIWIL3 (32414 downstream)																							AGGCATGCTGTGCTCTAACTG	0.403													t|||	2768	0.552716	0.5847	0.6427	5008	,	,		17951	0.4415		0.506	False		,,,				2504	0.6084				.													.	.			0			.																																									SO:0001628	intergenic_variant	641379	.			ATGCTGTGCTCTA																													22.37:g.25082586T>G			Somatic	58	0	0		WXS	Illumina HiSeq	Phase_1	69	0.09	6	.	0		0		RNA	SNP		37																																																																																					0	0.403										
ARL5AP4	641379	bcgsc.ca	37	22	25082635	25082635	+	IGR	SNP	C	C	T	rs5760578	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:25082635C>T								GGT1 (57663 upstream) : PIWIL3 (32365 downstream)																							GACGATGTCACGACTTTAGAT	0.378													c|||	2771	0.553315	0.5847	0.6427	5008	,	,		19159	0.4474		0.507	False		,,,				2504	0.6043				.													.	.			0			.																																									SO:0001628	intergenic_variant	641379	.			ATGTCACGACTTT																													22.37:g.25082635C>T			Somatic	71	0	0		WXS	Illumina HiSeq	Phase_1	79	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.378										
Unknown	0	bcgsc.ca	37	22	41470522	41470522	+	IGR	SNP	G	G	A	rs8136923	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:41470522G>A								Y_RNA (8872 upstream) : EP300 (17267 downstream)																							GCGCCTCGGGGCAGTGGAACC	0.577													G|||	1256	0.250799	0.1331	0.5346	5008	,	,		21802	0.0536		0.3052	False		,,,				2504	0.3558				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCGGGGCAGTGG																													22.37:g.41470522G>A			Somatic	37	0	0		WXS	Illumina HiSeq	Phase_1	37	0.14	5	.	6	0.00	0		RNA	SNP		37																																																																																					0	0.577										
LL22NC03-75H12.2	101927722	bcgsc.ca	37	22	47857537	47857537	+	Missense_Mutation	SNP	T	T	C	rs130877	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:47857537T>C	ENST00000405369.3	-	3	494	c.163A>G	c.(163-165)Aag>Gag	p.K55E	LL22NC03-75H12.2_ENST00000481625.1_5'Flank																							TGTGTTCCCTTAGTTGCACCT	0.463													C|||	1598	0.319089	0.5	0.2493	5008	,	,		17037	0.1468		0.3807	False		,,,				2504	0.2382				.													.	.			0			.																																									SO:0001583	missense	0	.			TTCCCTTAGTTGC																												ENST00000405369.3:c.163A>G	22.37:g.47857537T>C	ENSP00000385262:p.Lys55Glu		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_1	188	0.05	10	.	0		0		Missense_Mutation	SNP	ENST00000405369.3	37		741	0.3392857142857143	249	0.5060975609756098	103	0.2845303867403315	90	0.15734265734265734	299	0.3944591029023747	C	3.132	-0.178146	0.06380	.	.	ENSG00000218357	ENST00000405369	.	.	.	2.78	-1.83	0.07833	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.45160	-0.9280	4	0.87932	D	0	.	8.5324	0.33342	0.0:0.4941:0.0:0.5059	rs130877	.	.	.	E	55	.	ENSP00000385262:K55E	K	-	1	0	LL22NC03-75H12.2	46236201	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.131000	0.00590	-0.991000	0.03476	-1.163000	0.01768	AAG			0.463	LL22NC03-75H12.2-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000317561.3			
LL22NC03-75H12.2	101927722	bcgsc.ca	37	22	47857551	47857551	+	Missense_Mutation	SNP	T	T	G	rs130878	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:47857551T>G	ENST00000405369.3	-	3	480	c.149A>C	c.(148-150)aAc>aCc	p.N50T	LL22NC03-75H12.2_ENST00000481625.1_5'Flank																							TGCACCTCTGTTCTTGAGCTT	0.443													G|||	1921	0.383586	0.7073	0.2666	5008	,	,		17859	0.1825		0.3807	False		,,,				2504	0.2393				.													.	.			0			.																																									SO:0001583	missense	0	.			CCTCTGTTCTTGA																												ENST00000405369.3:c.149A>C	22.37:g.47857551T>G	ENSP00000385262:p.Asn50Thr		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_1	193	0.05	9	.	0		0		Missense_Mutation	SNP	ENST00000405369.3	37		865	0.39606227106227104	340	0.6910569105691057	107	0.2955801104972376	119	0.20804195804195805	299	0.3944591029023747	G	4.294	0.053827	0.08291	.	.	ENSG00000218357	ENST00000405369	.	.	.	2.83	2.83	0.33086	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.40646	-0.9552	4	0.87932	D	0	.	7.2341	0.26059	0.0:0.0:0.7352:0.2648	rs130878;rs17830592;rs59849447;rs130878	.	.	.	T	50	.	ENSP00000385262:N50T	N	-	2	0	LL22NC03-75H12.2	46236215	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.548000	0.23314	0.752000	0.32923	-0.187000	0.12897	AAC			0.443	LL22NC03-75H12.2-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000317561.3			
LL22NC03-75H12.2	101927722	bcgsc.ca	37	22	47857576	47857576	+	Silent	SNP	A	A	G	rs130879	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr22:47857576A>G	ENST00000405369.3	-	3	455	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	LL22NC03-75H12.2_ENST00000481625.1_5'Flank																							TCTTTCTGCAAAACTAAACCA	0.398													A|||	1598	0.319089	0.5	0.2493	5008	,	,		17609	0.1468		0.3807	False		,,,				2504	0.2382				.													.	.			0			.																																									SO:0001819	synonymous_variant	0	.			TCTGCAAAACTAA																												ENST00000405369.3:c.124T>C	22.37:g.47857576A>G			Somatic	162	0	0		WXS	Illumina HiSeq	Phase_1	189	0.04	8	.	0		0		Silent	SNP	ENST00000405369.3	37																																																																																						0.398	LL22NC03-75H12.2-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000317561.3			
Unknown	0	bcgsc.ca	37	22	51193572	51193572	+	IGR	SNP	A	A	G	rs138661035	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	149	0	0		WXS	Illumina HiSeq	Phase_1	157	0.07	11	.	18	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	230	0.0130434783	3		WXS	Illumina HiSeq	Phase_1	236	0.06	15	.	26	0.00	0		RNA	SNP		37																																																																																					0	0.443										
RHBDF1P1	131973	bcgsc.ca	37	3	14614889	14614889	+	IGR	SNP	T	T	C	rs11707648	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:14614889T>C								GRIP2 (33008 upstream) : AC090952.5 (74811 downstream)																							TCCCGCGGGATGGTCATCTGG	0.597													C|||	874	0.174521	0.2345	0.1801	5008	,	,		20603	0.0853		0.1451	False		,,,				2504	0.2117				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCGGGATGGTCAT																													3.37:g.14614889T>C			Somatic	50	0	0		WXS	Illumina HiSeq	Phase_1	30	0.13	4	.	6	0.00	0		RNA	SNP		37																																																																																					0	0.597										
RHBDF1P1	131973	bcgsc.ca	37	3	14615601	14615601	+	IGR	SNP	A	A	C	rs9840720	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:14615601A>C								GRIP2 (33720 upstream) : AC090952.5 (74099 downstream)																							GGTTCCACAGAATCGAGTCCA	0.567													C|||	875	0.17472	0.2345	0.1801	5008	,	,		20869	0.0853		0.1451	False		,,,				2504	0.2127				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCACAGAATCGAG																													3.37:g.14615601A>C			Somatic	109	0	0		WXS	Illumina HiSeq	Phase_1	116	0.08	9	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.567										
RHBDF1P1	131973	bcgsc.ca	37	3	14615612	14615612	+	IGR	SNP	T	T	C	rs9823227	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:14615612T>C								GRIP2 (33731 upstream) : AC090952.5 (74088 downstream)																							ATCGAGTCCATCGTTTCATGC	0.562													C|||	874	0.174521	0.2345	0.1801	5008	,	,		20786	0.0853		0.1451	False		,,,				2504	0.2117				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTCCATCGTTTC																													3.37:g.14615612T>C			Somatic	95	0	0		WXS	Illumina HiSeq	Phase_1	105	0.08	8	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.562										
THRAP3P1	391524	bcgsc.ca	37	3	31496295	31496295	+	IGR	SNP	T	T	G	rs724607	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:31496295T>G								AC099540.1 (58772 upstream) : STT3B (77834 downstream)																							CTAAAGAGACTAACTGAGCAG	0.433													G|||	557	0.111222	0.0772	0.1081	5008	,	,		20135	0.2579		0.0427	False		,,,				2504	0.0787				.													.	.			0			.																																									SO:0001628	intergenic_variant	391524	.			AGAGACTAACTGA																													3.37:g.31496295T>G			Somatic	134	0.0074626866	1		WXS	Illumina HiSeq	Phase_1	93	0.09	8	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.433										
HSPD1P6	645548	bcgsc.ca	37	3	36809119	36809119	+	RNA	SNP	G	G	A	rs9311135	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:36809119G>A	ENST00000424886.1	-	0	571									heat shock 60kDa protein 1 (chaperonin) pseudogene 6																		ACCAACCTTTGGCATAGCTAT	0.393													A|||	2905	0.580072	0.6974	0.5476	5008	,	,		22628	0.5486		0.5199	False		,,,				2504	0.5389				.													.	.			0			.																																											645548	.			ACCTTTGGCATAG			3p22.3	2010-06-25	2002-08-29	2008-09-22	ENSG00000230067	ENSG00000230067			5267	pseudogene	pseudogene			"""heat shock 60kD protein 1 (chaperonin) pseudogene 6"""	HSPDP6			Standard	NG_008828		Approved	HSPD1-6P			OTTHUMG00000155803		3.37:g.36809119G>A			Somatic	119	0	0		WXS	Illumina HiSeq	Phase_1	96	0.06	6	.	2	0.00	0		RNA	SNP	ENST00000424886.1	37																																																																																						0.393	HSPD1P6-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000341724.1		XR_017400	
GOLGA4	2803	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	37340359	37340359	+	Missense_Mutation	SNP	C	C	G			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:37340359C>G	ENST00000361924.2	+	8	1224	c.850C>G	c.(850-852)Ctc>Gtc	p.L284V	GOLGA4_ENST00000435830.2_3'UTR|GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.L306V	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	284	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ACTGGAAACACTCCAGCAAAG	0.368																																					p.L306V													.	.			0			c.C916G												104.0	104.0	104.0					3																	37340359		2203	4300	6503	SO:0001583	missense	2803	exon9			GAAACACTCCAGC	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.850C>G	3.37:g.37340359C>G	ENSP00000354486:p.Leu284Val		Somatic	285	0	0		WXS	Illumina HiSeq	.	253	0.20	50	NM_001172713	134	0.31	41	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325942	0.60743	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000450863;ENST00000437131	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.22	5.22	0.72569	.	0.000000	0.32736	N	0.005717	T	0.63663	0.2530	M	0.74258	2.255	0.30335	N	0.786283	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.78314	0.991;0.991;0.99	T	0.61510	-0.7048	10	0.23891	T	0.37	.	17.3166	0.87226	0.0:1.0:0.0:0.0	.	284;306;284	Q13439-4;F8W8Q7;Q13439	.;.;GOGA4_HUMAN	V	284;306;289;155	ENSP00000354486:L284V;ENSP00000349305:L306V;ENSP00000387633:L289V;ENSP00000405842:L155V	ENSP00000349305:L306V	L	+	1	0	GOLGA4	37315363	1.000000	0.71417	0.460000	0.27093	0.705000	0.40729	3.153000	0.50685	2.613000	0.88420	0.643000	0.83706	CTC			0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000253339.2		NM_002078	
ITIH4	3700	hgsc.bcm.edu	37	3	52852482	52852482	+	Silent	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:52852482G>T	ENST00000266041.4	-	18	2244	c.2148C>A	c.(2146-2148)atC>atA	p.I716I	ITIH4_ENST00000485816.1_Silent_p.I721I|ITIH4_ENST00000467462.1_5'Flank|ITIH4_ENST00000406595.1_Silent_p.I686I|ITIH4_ENST00000346281.5_Silent_p.I686I|RP5-966M1.6_ENST00000468472.1_3'UTR	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	716					acute-phase response (GO:0006953)|hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)|response to cytokine (GO:0034097)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GGGCACCTTCGATTTTCATAT	0.552																																					p.I716I													.	.			0			c.C2148A												54.0	51.0	52.0					3																	52852482		2203	4299	6502	SO:0001819	synonymous_variant	3700	exon18			ACCTTCGATTTTC	D38535	CCDS2865.1, CCDS54596.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055955	ENSG00000055955			6169	protein-coding gene	gene with protein product	"""plasma Kallikrein-sensitive glycoprotein"""	600564	"""inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)"""	ITIHL1		9480842, 7805892	Standard	NM_002218		Approved	IHRP, H4P	uc003dfz.3	Q14624	OTTHUMG00000159023	ENST00000266041.4:c.2148C>A	3.37:g.52852482G>T			Somatic	96	0	0		WXS	Illumina HiSeq	.	119	0.04	5	NM_002218	26	0.00	0	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1																																																																																					0.552	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000317715.1		NM_002218	
CYP51A1P1	83528	bcgsc.ca	37	3	82855676	82855676	+	IGR	SNP	G	G	A	rs12636791	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:82855676G>A								RP11-260O18.1 (342850 upstream) : None (None downstream)																							TTTGATCTTCGTTTGTAATGG	0.348													G|||	799	0.159545	0.0961	0.1499	5008	,	,		18918	0.2669		0.1491	False		,,,				2504	0.1524				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCTTCGTTTGTA																													3.37:g.82855676G>A			Somatic	35	0	0		WXS	Illumina HiSeq	Phase_1	37	0.19	7	.	0		0		RNA	SNP		37																																																																																					0	0.348										
CYP51A1P1	83528	bcgsc.ca	37	3	82856698	82856698	+	IGR	SNP	G	G	A	rs6782717	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:82856698G>A								RP11-260O18.1 (343872 upstream) : None (None downstream)																							ACTTTTTAACGTTTTCTTCTG	0.398													A|||	1979	0.395168	0.7307	0.4006	5008	,	,		16483	0.0754		0.3817	False		,,,				2504	0.2812				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTAACGTTTTCT																													3.37:g.82856698G>A			Somatic	178	0.0056179775	1		WXS	Illumina HiSeq	Phase_1	175	0.07	13	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	3	109635659	109635659	+	IGR	SNP	C	C	T	rs605795	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:109635659C>T								RP11-457K10.1 (105951 upstream) : RP11-119D18.1 (610669 downstream)																							CATTTGTGTCCTCTTGATCAC	0.393													T|||	3123	0.623602	0.5333	0.5865	5008	,	,		23367	0.6944		0.6262	False		,,,				2504	0.6963				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTGTCCTCTTGA																													3.37:g.109635659C>T			Somatic	40	0	0		WXS	Illumina HiSeq	Phase_1	31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.393										
NAP1L1P3	100130335	bcgsc.ca	37	3	120525556	120525556	+	IGR	SNP	G	G	C	rs115209237	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:120525556G>C								GTF2E1 (23640 upstream) : RP11-500K19.1 (26730 downstream)																							ATGAACCAAAGAAAGATCAAA	0.408													.|||	48	0.00958466	0.0	0.0187	5008	,	,		21262	0.0		0.0199	False		,,,				2504	0.0153				.													.	.			0			.																																									SO:0001628	intergenic_variant	100130335	.			ACCAAAGAAAGAT																													3.37:g.120525556G>C			Somatic	47	0	0		WXS	Illumina HiSeq	Phase_1	45	0.13	6	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.408										
PSMC1P7	646085	bcgsc.ca	37	3	161047583	161047583	+	IGR	SNP	T	T	C	rs115806772	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:161047583T>C								NMD3 (76263 upstream) : SPTSSB (14996 downstream)																							ATGCACCTTGTGGCTGAGCAG	0.493													T|||	101	0.0201677	0.0257	0.0058	5008	,	,		19009	0.0198		0.0209	False		,,,				2504	0.0225				.													.	.			0			.																																									SO:0001628	intergenic_variant	646085	.			ACCTTGTGGCTGA																													3.37:g.161047583T>C			Somatic	24	0	0		WXS	Illumina HiSeq	Phase_1	19	0.21	4	.	0		0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	3	195346477	195346477	+	IGR	SNP	C	C	T	rs7631117	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr3:195346477C>T								APOD (35401 upstream) : RP11-141C7.4 (20383 downstream)																							CTCATCCCCACGGAAGGGGTG	0.532																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	200958	.			TCCCCACGGAAGG																													3.37:g.195346477C>T			Somatic	294	0.0034013605	1		WXS	Illumina HiSeq	Phase_1	322	0.12	39	.	2	0.00	0		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	.	10.61	1.398900	0.25291	.	.	ENSG00000176945	ENST00000381954	.	.	.	0.705	0.705	0.18127	.	.	.	.	.	T	0.36880	0.0983	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.35649	-0.9780	5	0.66056	D	0.02	.	4.8054	0.13317	0.0:1.0:0.0:0.0	rs7631117	.	.	.	M	260	.	ENSP00000371380:T260M	T	+	2	0	MUC20	196827766	0.000000	0.05858	0.053000	0.19242	0.156000	0.22039	-0.457000	0.06745	0.680000	0.31366	0.152000	0.16155	ACG		0	0.532										
OR7E85P	442105	bcgsc.ca;mdanderson.org	37	4	9486098	9486098	+	IGR	SNP	C	C	G	rs114281488	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	195	0	0		WXS	Illumina HiSeq	Phase_1	133	0.09	12	.	0		0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	4	43900983	43900983	+	IGR	SNP	T	T	C	rs6830030	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:43900983T>C								RN7SL193P (35420 upstream) : RP11-663P9.1 (81039 downstream)																							GCCAAGATGTTGTTCCCATAG	0.483													C|||	766	0.152955	0.4266	0.0634	5008	,	,		14587	0.0387		0.0417	False		,,,				2504	0.0787				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGATGTTGTTCCC																													4.37:g.43900983T>C			Somatic	101	0	0		WXS	Illumina HiSeq	Phase_1	62	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.483										
Unknown	0	bcgsc.ca	37	4	43900995	43900995	+	IGR	SNP	A	A	G	rs10019693	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:43900995A>G								RN7SL193P (35432 upstream) : RP11-663P9.1 (81027 downstream)																							TTCCCATAGTATAAGCCGTCG	0.493													A|||	719	0.14357	0.3926	0.062	5008	,	,		14325	0.0387		0.0408	False		,,,				2504	0.0787				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATAGTATAAGCC																													4.37:g.43900995A>G			Somatic	105	0	0		WXS	Illumina HiSeq	Phase_1	62	0.10	6	.	0		0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	4	57627276	57627276	+	IGR	SNP	G	G	A	rs6844407	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:57627276G>A								HOPX (79211 upstream) : RN7SL492P (33239 downstream)																							TCCACATTCAGCTTCAAAAAT	0.398													G|||	1020	0.203674	0.3253	0.1196	5008	,	,		18282	0.1667		0.1571	False		,,,				2504	0.1851				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATTCAGCTTCAA																													4.37:g.57627276G>A			Somatic	107	0	0		WXS	Illumina HiSeq	Phase_1	84	0.13	11	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.398										
EXOC5P1	644548	bcgsc.ca	37	4	63682913	63682913	+	IGR	SNP	T	T	C	rs6551720|rs386675165	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:63682913T>C								AC110810.1 (221733 upstream) : RP11-257A22.1 (311115 downstream)																							ACCCAGACAATGGGCAGTGCA	0.393													C|||	2214	0.442093	0.4947	0.2262	5008	,	,		17823	0.7302		0.2445	False		,,,				2504	0.4305				.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			AGACAATGGGCAG																													4.37:g.63682913T>C			Somatic	109	0	0		WXS	Illumina HiSeq	Phase_1	83	0.10	8	.	0		0		RNA	SNP		37																																																																																					0	0.393										
EXOC5P1	644548	bcgsc.ca	37	4	63682934	63682934	+	IGR	SNP	C	C	T	rs6551721	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:63682934C>T								AC110810.1 (221754 upstream) : RP11-257A22.1 (311094 downstream)																							GGCTCAGAAACTGATGAAATA	0.388													T|||	2214	0.442093	0.4947	0.2262	5008	,	,		17705	0.7302		0.2445	False		,,,				2504	0.4305				.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			CAGAAACTGATGA																													4.37:g.63682934C>T			Somatic	117	0	0		WXS	Illumina HiSeq	Phase_1	88	0.13	11	.	0		0		RNA	SNP		37																																																																																					0	0.388										
EXOC5P1	644548	bcgsc.ca	37	4	63683038	63683038	+	IGR	SNP	C	C	T	rs6852768	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:63683038C>T								AC110810.1 (221858 upstream) : RP11-257A22.1 (310990 downstream)																							AGAAGTTGCACCTAATTGCCC	0.323													C|||	1164	0.232428	0.118	0.1643	5008	,	,		19845	0.3938		0.1948	False		,,,				2504	0.3078				.													.	.			0			.																																									SO:0001628	intergenic_variant	644548	.			GTTGCACCTAATT																													4.37:g.63683038C>T			Somatic	238	0	0		WXS	Illumina HiSeq	Phase_1	153	0.07	11	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.323										
Unknown	0	bcgsc.ca	37	4	70212704	70212704	+	IGR	SNP	G	G	A	rs6851810	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	97	0.0103092784	1		WXS	Illumina HiSeq	Phase_1	78	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.398										
IGBP1P4	391672	bcgsc.ca	37	4	83323062	83323062	+	RNA	SNP	T	T	C	rs7695741	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	122	0	0		WXS	Illumina HiSeq	Phase_1	99	0.06	6	.	0		0		RNA	SNP	ENST00000365570.1	37																																																																																						0.458	SNORD42.2-201	NOVEL	basic	snoRNA	snoRNA					
RCC2P8	100129714	bcgsc.ca	37	4	109710728	109710728	+	RNA	SNP	C	C	T	rs13137797	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:109710728C>T	ENST00000581341.1	-	0	0																											ACATTATCTGCGCGGGGCTGT	0.532													C|||	1697	0.338858	0.3744	0.2911	5008	,	,		18925	0.372		0.3966	False		,,,				2504	0.2311				.													.	.			0			.																																											100129714	.			TATCTGCGCGGGG																													4.37:g.109710728C>T			Somatic	107	0	0		WXS	Illumina HiSeq	Phase_1	76	0.12	9	.	1	0.00	0		RNA	SNP	ENST00000581341.1	37																																																																																						0.532	AC097473.1-201	NOVEL	basic	miRNA	miRNA					
TOX4P1	285412	bcgsc.ca	37	4	113377127	113377127	+	IGR	SNP	G	G	T	rs231266	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:113377127G>T								ALPK1 (13365 upstream) : NEUROG2 (57544 downstream)																							TCACAGGGCCGTCACACCTCT	0.507													T|||	3146	0.628195	0.7126	0.4957	5008	,	,		19265	0.6508		0.6292	False		,,,				2504	0.5838				.													.	.			0			.																																									SO:0001628	intergenic_variant	285412	.			AGGGCCGTCACAC																													4.37:g.113377127G>T			Somatic	42	0	0		WXS	Illumina HiSeq	Phase_1	41	0.15	6	.	0		0		RNA	SNP		37																																																																																					0	0.507										
TOX4P1	285412	bcgsc.ca	37	4	113377710	113377710	+	IGR	SNP	T	T	G	rs231267	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:113377710T>G								ALPK1 (13948 upstream) : NEUROG2 (56961 downstream)																							AAAGCAGAAGTTCCCAAAGAA	0.443													G|||	3148	0.628594	0.7126	0.4986	5008	,	,		21767	0.6508		0.6282	False		,,,				2504	0.5849				.													.	.			0			.																																									SO:0001628	intergenic_variant	285412	.			CAGAAGTTCCCAA																													4.37:g.113377710T>G			Somatic	90	0	0		WXS	Illumina HiSeq	Phase_1	73	0.10	7	.	0		0		RNA	SNP		37																																																																																					0	0.443										
Unknown	0	bcgsc.ca	37	4	120315906	120315906	+	IGR	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	172	0.011627907	2		WXS	Illumina HiSeq	Phase_1	121	0.11	13	.	0		0		RNA	SNP		37																																																																																					0	0.408										
Unknown	0	bcgsc.ca	37	4	139402514	139402514	+	IGR	SNP	T	T	C	rs13101897	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr4:139402514T>C								LINC00500 (44491 upstream) : RP11-173E2.2 (183364 downstream)																							TACTGTTCATTTGTGGGACTC	0.488													T|||	1995	0.398363	0.3086	0.4409	5008	,	,		18957	0.6657		0.3151	False		,,,				2504	0.2996				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCATTTGTGGG																													4.37:g.139402514T>C			Somatic	29	0	0		WXS	Illumina HiSeq	Phase_1	24	0.25	6	.	0		0		RNA	SNP		37																																																																																					0	0.488										
Unknown	0	bcgsc.ca	37	4	189660460	189660460	+	IGR	SNP	G	G	C	rs60608362	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	189	0.0052910053	1		WXS	Illumina HiSeq	Phase_1	133	0.08	11	.	45	0.00	0		RNA	SNP		37																																																																																					0	0.358										
Unknown	0	bcgsc.ca	37	5	10664632	10664632	+	IGR	SNP	A	A	G	rs12523340	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr5:10664632A>G								RP11-215G15.5 (6704 upstream) : DAP (14709 downstream)																							TCTGTGGTCAACTTCACATAA	0.502													G|||	1155	0.230631	0.2042	0.2666	5008	,	,		19521	0.2321		0.2942	False		,,,				2504	0.1738				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGTCAACTTCAC																													5.37:g.10664632A>G			Somatic	152	0	0		WXS	Illumina HiSeq	Phase_1	110	0.09	10	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	5	10664999	10664999	+	IGR	SNP	C	C	G	rs111384023	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr5:10664999C>G								RP11-215G15.5 (7071 upstream) : DAP (14342 downstream)																							GCTCGGGGCCCGTGGCGGTGT	0.517													g|||	1408	0.28115	0.3222	0.2824	5008	,	,		17960	0.2748		0.2972	False		,,,				2504	0.2147				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGGCCCGTGGCG																													5.37:g.10664999C>G			Somatic	120	0	0		WXS	Illumina HiSeq	Phase_1	86	0.13	11	.	0		0		RNA	SNP		37																																																																																					0	0.517										
Unknown	0	bcgsc.ca	37	5	97361783	97361783	+	IGR	SNP	G	G	A	rs4355547	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr5:97361783G>A								RP11-455B3.1 (103384 upstream) : AC008834.1 (60180 downstream)																							caggatcatcgaggtcgcacc	0.463																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCATCGAGGTCG																													5.37:g.97361783G>A			Somatic	69	0	0		WXS	Illumina HiSeq	Phase_1	33	0.12	4	.	0		0		RNA	SNP		37																																																																																					0	0.463										
PCDHB4	56131	ucsc.edu;bcgsc.ca	37	5	140502343	140502344	+	Missense_Mutation	DNP	CC	CC	TT	rs3733697|rs3733698|rs377479392	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	125	0.008	1		WXS	Illumina HiSeq		75	0.11	8	NM_018938	0		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	
FLT4	2324	hgsc.bcm.edu	37	5	180048756	180048756	+	Silent	SNP	G	G	A			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr5:180048756G>A	ENST00000261937.6	-	13	1884	c.1806C>T	c.(1804-1806)caC>caT	p.H602H	FLT4_ENST00000393347.3_Silent_p.H602H|FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.H602H	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	602	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GCGGGTTCCCGTGCGCATCGT	0.667																																					p.H602H	Colon(97;1075 1466 27033 27547 35871)												.	.			0			c.C1806T												81.0	70.0	73.0					5																	180048756		2203	4300	6503	SO:0001819	synonymous_variant	2324	exon13			GTTCCCGTGCGCA	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1806C>T	5.37:g.180048756G>A			Somatic	85	0	0		WXS	Illumina HiSeq	.	73	0.05	4	NM_182925	6	0.00	0	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																					0.667	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253527.4			
CDYL	9425	bcgsc.ca	37	6	4735035	4735035	+	Missense_Mutation	SNP	T	T	C	rs13196069	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_1	79	0.06	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	
Unknown	0	bcgsc.ca	37	6	7517131	7517131	+	IGR	SNP	A	A	T	rs2798162	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:7517131A>T								RIOK1 (98861 upstream) : RP3-512B11.3 (23552 downstream)																							GTACATGCAGAAGTGACGGGT	0.517													T|||	1372	0.273962	0.1641	0.3588	5008	,	,		20450	0.1855		0.3479	False		,,,				2504	0.3773				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGCAGAAGTGAC																													6.37:g.7517131A>T			Somatic	56	0	0		WXS	Illumina HiSeq	Phase_1	41	0.15	6	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.517										
DEK	7913	bcgsc.ca	37	6	18264096	18264096	+	Missense_Mutation	SNP	C	C	G	rs147127829	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:18264096C>G	ENST00000397239.3	-	2	570	c.123G>C	c.(121-123)gaG>gaC	p.E41D	DEK_ENST00000244776.7_Missense_Mutation_p.E41D	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	41	Asp/Glu-rich (highly acidic).				chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			cctcctcctcctcgtcgtcct	0.562			T	NUP214	AML								C|||	10	0.00199681	0.0068	0.0	5008	,	,		14423	0.0		0.0	False		,,,				2504	0.001				p.E41D				Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31		0			c.G123C							-	ASP/GLU,ASP/GLU	8,4398	14.3+/-33.2	0,8,2195	43.0	47.0	45.0		123,123	-3.7	0.1	6	dbSNP_134	45	0,8600		0,0,4300	yes	missense,missense	DEK	NM_001134709.1,NM_003472.3	45,45	0,8,6495	GG,GC,CC		0.0,0.1816,0.0615	benign,benign	41/342,41/376	18264096	8,12998	2203	4300	6503	SO:0001583	missense	7913	exon2			CTCCTCCTCGTCG	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.123G>C	6.37:g.18264096C>G	ENSP00000380414:p.Glu41Asp		Somatic	130	0.0076923077	1		WXS	Illumina HiSeq	Phase_1	157	0.05	8	NM_003472	79	0.00	0	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Missense_Mutation	SNP	ENST00000397239.3	37	CCDS34344.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.267	0.417416	0.11870	0.001816	0.0	ENSG00000124795	ENST00000397239;ENST00000244776;ENST00000515742	T;T;T	0.51817	0.76;0.85;0.69	4.57	-3.65	0.04502	.	0.440668	0.20131	N	0.098587	T	0.09598	0.0236	L	0.48642	1.525	0.22880	N	0.998611	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38585	-0.9654	10	0.12766	T	0.61	-5.206	1.3254	0.02124	0.2162:0.3697:0.1081:0.306	.	41;41	B4DN37;P35659	.;DEK_HUMAN	D	41;41;46	ENSP00000380414:E41D;ENSP00000244776:E41D;ENSP00000423553:E46D	ENSP00000244776:E41D	E	-	3	2	DEK	18372075	0.003000	0.15002	0.050000	0.19076	0.529000	0.34654	-2.192000	0.01245	-1.460000	0.01911	-2.294000	0.00264	GAG			0.562	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000039962.4			
Unknown	0	bcgsc.ca	37	6	23972696	23972696	+	IGR	SNP	G	G	T	rs34725714	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	110	0	0		WXS	Illumina HiSeq	Phase_1	87	0.09	8	.	0		0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	6	23972870	23972870	+	IGR	SNP	T	T	A	rs35353646	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:23972870T>A								RP11-439H9.1 (626082 upstream) : NRSN1 (153479 downstream)																							TTGAAGATACTCACAGGGAAG	0.537													T|||	882	0.176118	0.264	0.1297	5008	,	,		18445	0.0675		0.162	False		,,,				2504	0.2168				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGATACTCACAGG																													6.37:g.23972870T>A			Somatic	57	0	0		WXS	Illumina HiSeq	Phase_1	57	0.09	5	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.537										
ZNF322	79692	bcgsc.ca	37	6	26637724	26637724	+	Missense_Mutation	SNP	T	T	C	rs139332558	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:26637724T>C	ENST00000415922.2	-	4	1703	c.1058A>G	c.(1057-1059)tAc>tGc	p.Y353C	ZNF322_ENST00000471278.1_Missense_Mutation_p.Y353C|RP11-457M11.2_ENST00000456172.1_RNA|ZNF322_ENST00000461899.1_5'Flank	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		Somatic	506	0.0039525692	2		WXS	Illumina HiSeq	Phase_1	465	0.03	16	NM_001242797	67	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	bcgsc.ca	37	6	28331127	28331128	+	Missense_Mutation	DNP	AA	AA	GC	rs13201752|rs13201753|rs371085669	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	AA	AA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_1	71	0.07	5	NM_024493	34	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	120	0.0083333333	1		WXS	Illumina HiSeq	Phase_1	91	0.11	10	.	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-U	352965	bcgsc.ca	37	6	29901899	29901899	+	IGR	SNP	C	C	G	rs2524004	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:29901899C>G								HLA-G (102997 upstream) : HLA-A (7137 downstream)																							CGCCCTAAACCAGGACCTGAG	0.557													g|||	4568	0.912141	0.9244	0.8934	5008	,	,		15014	0.9722		0.83	False		,,,				2504	0.9315				.													.	.			0			.																																									SO:0001628	intergenic_variant	352965	.			CTAAACCAGGACC																													6.37:g.29901899C>G			Somatic	21	0	0		WXS	Illumina HiSeq	Phase_1	29	0.24	7	.	0		0		RNA	SNP		37																																																																																					0	0.557										
HLA-U	352965	bcgsc.ca	37	6	29901919	29901919	+	IGR	SNP	T	T	C	rs1611304	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:29901919T>C								HLA-G (103017 upstream) : HLA-A (7117 downstream)																							GCTCTTGGACTGCGGCGGCCA	0.572													N|||	4568	0.912141	0.9244	0.8934	5008	,	,		14531	0.9722		0.83	False		,,,				2504	0.9315				.													.	.			0			.																																									SO:0001628	intergenic_variant	352965	.			TTGGACTGCGGCG																													6.37:g.29901919T>C			Somatic	24	0	0		WXS	Illumina HiSeq	Phase_1	33	0.21	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.572										
HLA-C	3107	bcgsc.ca	37	6	31236853	31236854	+	3'UTR	DNP	GT	GT	AC	rs1049709|rs1065711|rs386698953	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:31236853_31236854GT>AC	ENST00000376228.5	-	0	1207_1208				HLA-C_ENST00000383329.3_3'UTR	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C						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)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACACATTCAGGTGCCTTTGCAG	0.55																																					p.T397V													.	HLA-C	92		0			.																																									SO:0001624	3_prime_UTR_variant	3107	.			ATTCAGGTGCCTT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.1099_1099delinsAC	6.37:g.31236853_31236854delinsAC			Somatic	176	0	0		WXS	Illumina HiSeq	Phase_1	174	0.10	17	.	3197	0.00	0	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	DNP	ENST00000376228.5	37	CCDS34393.1																																																																																					0.550	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076281.3		NM_002117	
HLA-DQA1	3117	bcgsc.ca	37	6	32610008	32610009	+	Missense_Mutation	DNP	CC	CC	TG	rs2308890|rs2308891	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:32610008_32610009CC>TG	ENST00000343139.5	+	3	693_694	c.591_592CC>TG	c.(589-594)gaCCag>gaTGag	p.Q198E	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.Q198E|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.Q198E	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	197	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GGGGCCTGGACCAGCCTCTTCT	0.446																																					p.Q198E													.	HLA-DQA1	52		0			c.C592G																																									SO:0001583	missense	3117	exon3			CCTGGACCAGCCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	Exception_encountered	6.37:g.32610008_32610009delinsTG	ENSP00000339398:p.Gln198Glu		Somatic	511	0	0		WXS	Illumina HiSeq	Phase_1	468	0.03	15	NM_002122	669	0.00	0	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	DNP	ENST00000343139.5	37	CCDS4752.1																																																																																					0.446	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076176.3		NM_002122	
ADH5P4	642443	bcgsc.ca	37	6	66546941	66546941	+	IGR	SNP	A	A	G	rs61732140	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	267	0	0		WXS	Illumina HiSeq	Phase_1	234	0.06	13	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	181	0.0055248619	1		WXS	Illumina HiSeq	Phase_1	139	0.04	6	.	0		0		RNA	SNP		37																																																																																					0	0.453										
NUFIP1P	89761	bcgsc.ca	37	6	66803535	66803535	+	IGR	SNP	C	C	A	rs2881644	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:66803535C>A								EYS (386417 upstream) : AC002485.1 (265782 downstream)																							CTTTTCAAAACTTTTCTTTCG	0.358													c|||	3373	0.673522	0.7753	0.6499	5008	,	,		19104	0.6458		0.6491	False		,,,				2504	0.6063				.													.	.			0			.																																									SO:0001628	intergenic_variant	89761	.			TCAAAACTTTTCT																													6.37:g.66803535C>A			Somatic	162	0	0		WXS	Illumina HiSeq	Phase_1	123	0.09	11	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.358										
Unknown	0	bcgsc.ca	37	6	80775738	80775738	+	IGR	SNP	C	C	G	rs3812151	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:80775738C>G								TTK (23494 upstream) : BCKDHB (40625 downstream)																							TGATACATCTCCTGGGGAGAC	0.478													C|||	1824	0.364217	0.1006	0.5519	5008	,	,		20443	0.6131		0.3429	False		,,,				2504	0.3528				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACATCTCCTGGGG																													6.37:g.80775738C>G			Somatic	89	0	0		WXS	Illumina HiSeq	Phase_1	106	0.07	7	.	56	0.00	0		RNA	SNP		37																																																																																					0	0.478										
Unknown	0	bcgsc.ca	37	6	85996401	85996401	+	IGR	SNP	C	C	T	rs313229	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	222	0	0		WXS	Illumina HiSeq	Phase_1	224	0.05	12	.	8	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	133	0	0		WXS	Illumina HiSeq	Phase_1	148	0.09	14	.	0		0		RNA	SNP	ENST00000384579.1	37																																																																																						0.423	RNU4-70P-201	KNOWN	basic	snRNA	snRNA					
MICAL1	64780	bcgsc.ca	37	6	109767930	109767931	+	Missense_Mutation	DNP	GC	GC	TT	rs552227069|rs59056467|rs9320288|rs35260632	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:109767930_109767931GC>TT	ENST00000358807.3	-	18	2583_2584	c.2272_2273GC>AA	c.(2272-2274)GCg>AAg	p.A758K	MICAL1_ENST00000358577.3_Missense_Mutation_p.A672K|MICAL1_ENST00000368952.4_Missense_Mutation_p.A777K	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	758			A -> E (in dbSNP:rs9320288).|A -> K (requires 2 nucleotide substitutions; dbSNP:rs35260632). {ECO:0000269|PubMed:11827972, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|A -> S (in dbSNP:rs59056467).|A -> T (in dbSNP:rs59056467).		actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		GCTGCCTTCCGCTTTGTGGTCT	0.574																																					p.A777K													.	MICAL1	79		0			c.G2272A																																									SO:0001583	missense	64780	exon18			CCTTCCGCTTTGT	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2272_2273delinsTT	6.37:g.109767930_109767931delinsTT	ENSP00000351664:p.Ala758Lys		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_1	187	0.04	8	NM_022765	457	0.00	0	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	DNP	ENST00000358807.3	37	CCDS5076.1																																																																																					0.574	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041759.2		NM_022765	
Unknown	0	bcgsc.ca	37	6	111244963	111244963	+	IGR	SNP	A	A	G	rs781496	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:111244963A>G								AMD1 (28047 upstream) : GTF3C6 (34799 downstream)																							ATGAGAGTGAAGATGAAGATG	0.502													G|||	1380	0.275559	0.2496	0.134	5008	,	,		19778	0.3433		0.2157	False		,,,				2504	0.4029				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGTGAAGATGAA																													6.37:g.111244963A>G			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_1	49	0.10	5	.	0		0		RNA	SNP		37																																																																																					0	0.502										
Unknown	0	bcgsc.ca	37	6	111245074	111245074	+	IGR	SNP	T	T	C	rs781495	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:111245074T>C								AMD1 (28158 upstream) : GTF3C6 (34688 downstream)																							TGGATCTGGATGGGCCAAAGG	0.488													C|||	2141	0.427516	0.4735	0.1844	5008	,	,		20942	0.6548		0.2505	False		,,,				2504	0.4857				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTGGATGGGCCA																													6.37:g.111245074T>C			Somatic	85	0	0		WXS	Illumina HiSeq	Phase_1	70	0.09	6	.	0		0		RNA	SNP		37																																																																																					0	0.488										
RPL35AP3	387074	bcgsc.ca;mdanderson.org	37	6	137295352	137295352	+	IGR	SNP	C	C	T	rs2876354|rs374217857	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:137295352C>T								Y_RNA (39348 upstream) : RP11-55K22.5 (7949 downstream)																							GCCTTCCAGACGTATTTCCTT	0.488													c|||	2043	0.407947	0.2481	0.4928	5008	,	,		18245	0.4306		0.4891	False		,,,				2504	0.4571				.													.	.			0			.																																									SO:0001628	intergenic_variant	387074	.			TCCAGACGTATTT																													6.37:g.137295352C>T			Somatic	54	0	0		WXS	Illumina HiSeq	Phase_1	51	0.14	7	.	0		0		RNA	SNP		37																																																																																					0	0.488										
BTF3L4P3	391040	bcgsc.ca	37	6	137865140	137865140	+	IGR	SNP	A	A	G	rs9484059	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	87	0.0114942529	1		WXS	Illumina HiSeq	Phase_1	84	0.08	7	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.418										
SRP72P2	153932	bcgsc.ca	37	6	158658857	158658857	+	IGR	SNP	A	A	C	rs112542076	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	45	0	0		WXS	Illumina HiSeq	Phase_1	47	0.09	4	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.388										
SRP72P2	153932	bcgsc.ca	37	6	158658937	158658937	+	IGR	SNP	T	T	C	rs7753292	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:158658937T>C								GTF2H5 (38561 upstream) : RP11-732M18.3 (44357 downstream)																							TGAATATCTTTTGGATTTTGT	0.403													t|||	1656	0.330671	0.1044	0.4611	5008	,	,		19022	0.4573		0.4185	False		,,,				2504	0.3231				.													.	.			0			.																																									SO:0001628	intergenic_variant	153932	.			TATCTTTTGGATT																													6.37:g.158658937T>C			Somatic	60	0	0		WXS	Illumina HiSeq	Phase_1	66	0.08	5	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.403										
LOC101929297	101929297	bcgsc.ca	37	6	166653792	166653792	+	lincRNA	SNP	A	A	C	rs6931334	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr6:166653792A>C	ENST00000444219.1	+	0	72																											AAAAAGGAATAGAATTTCTGG	0.338													A|||	2494	0.498003	0.6271	0.4914	5008	,	,		19861	0.5863		0.4245	False		,,,				2504	0.3129				.													.	.			0			.																																											2789	.			AGGAATAGAATTT																													6.37:g.166653792A>C			Somatic	56	0	0		WXS	Illumina HiSeq	Phase_1	49	0.22	11	.	0		0		RNA	SNP	ENST00000444219.1	37																																																																																						0.338	RP4-655C5.4-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000043045.1			
ELFN1	392617	bcgsc.ca;mdanderson.org	37	7	1733102	1733102	+	Intron	SNP	G	G	T	rs4720922	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:1733102G>T	ENST00000424383.2	+	1	32				AC074389.6_ENST00000382528.1_Missense_Mutation_p.L144M|AC074389.7_ENST00000450458.1_lincRNA			P0C7U0	ELFN1_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 1						negative regulation of phosphatase activity (GO:0010923)|synapse organization (GO:0050808)	dendrite (GO:0030425)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)	1						GGTGCACCCAGACAGGTGCGT	0.567													G|||	921	0.183906	0.0083	0.2824	5008	,	,		22706	0.1627		0.2744	False		,,,				2504	0.2802				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CACCCAGACAGGT		CCDS59046.1	7p22.3	2013-02-11	2011-10-27	2011-10-27	ENSG00000225968	ENSG00000225968		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	33154	protein-coding gene	gene with protein product		614964	"""extracellular leucine-rich repeat and fibronectin type III containing 1"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 1"", ""protein phosphatase 1, regulatory subunit 28"""	PPP1R28		17868438	Standard	NM_001128636		Approved		uc010ksg.2	P0C7U0	OTTHUMG00000151495	ENST00000424383.2:c.-456+5316G>T	7.37:g.1733102G>T			Somatic	191	0	0		WXS	Illumina HiSeq	Phase_1	241	0.10	24	.	0		0	H3BS57	Missense_Mutation	SNP	ENST00000424383.2	37	CCDS59046.1	427	0.1955128205128205	3	0.006097560975609756	102	0.281767955801105	104	0.18181818181818182	218	0.287598944591029	G	8.260	0.810947	0.16537	.	.	ENSG00000205971	ENST00000382528	.	.	.	1.69	1.69	0.24217	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.65815	0.995	P	0.60682	0.878	T	0.05801	-1.0863	6	0.87932	D	0	.	6.8425	0.23971	0.0:0.0:1.0:0.0	rs4720922;rs58424792;rs4720922	144	A2RU56	.	M	144	.	ENSP00000371968:L144M	L	-	1	2	AC074389.6	1699628	0.002000	0.14202	0.007000	0.13788	0.025000	0.11179	0.495000	0.22483	1.237000	0.43756	0.462000	0.41574	CTG			0.567	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322893.2		NM_001128636	
Unknown	0	bcgsc.ca	37	7	9767725	9767725	+	IGR	SNP	G	G	T	rs72583761	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	168	0	0		WXS	Illumina HiSeq	Phase_1	219	0.08	18	.	2	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	126	0	0		WXS	Illumina HiSeq	Phase_1	134	0.08	11	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.572										
Unknown	0	bcgsc.ca	37	7	23603318	23603318	+	IGR	SNP	A	A	G	rs227944	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	310	0.0064516129	2		WXS	Illumina HiSeq	Phase_1	401	0.04	18	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.393										
ZNRF2P2	100271874	bcgsc.ca	37	7	29700039	29700039	+	RNA	SNP	C	C	T	rs1728603	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	142	0	0		WXS	Illumina HiSeq	Phase_1	184	0.11	20	.	1	0.00	0		RNA	SNP	ENST00000426767.1	37																																																																																						0.313	ZNRF2P2-003	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000327679.1		NR_027347	
HAUS6P1	653175	bcgsc.ca	37	7	53255471	53255471	+	IGR	SNP	A	A	G	rs6943510	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:53255471A>G								POM121L12 (150854 upstream) : RNU1-14P (178279 downstream)																							AGTTAAGCAGATACGAAACTT	0.313													G|||	4348	0.868211	0.9773	0.8228	5008	,	,		17983	0.9415		0.7147	False		,,,				2504	0.8354				.													.	.			0			.																																									SO:0001628	intergenic_variant	653175	.			AAGCAGATACGAA																													7.37:g.53255471A>G			Somatic	232	0	0		WXS	Illumina HiSeq	Phase_1	265	0.10	26	.	0		0		RNA	SNP		37																																																																																					0	0.313										
HAUS6P1	653175	bcgsc.ca	37	7	53256265	53256265	+	IGR	SNP	G	G	A	rs11972016	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:53256265G>A								POM121L12 (151648 upstream) : RNU1-14P (177485 downstream)																							CTTTCTTGTCGCAGTCAGTTT	0.398													A|||	1461	0.291733	0.3215	0.219	5008	,	,		18594	0.1935		0.332	False		,,,				2504	0.363				.													.	.			0			.																																									SO:0001628	intergenic_variant	653175	.			CTTGTCGCAGTCA																													7.37:g.53256265G>A			Somatic	280	0	0		WXS	Illumina HiSeq	Phase_1	249	0.07	18	.	18	0.00	0		RNA	SNP		37																																																																																					0	0.398										
HAUS6P1	653175	bcgsc.ca	37	7	53256324	53256324	+	IGR	SNP	T	T	C	rs35856447	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	241	0	0		WXS	Illumina HiSeq	Phase_1	234	0.05	12	.	15	0.00	0		RNA	SNP		37																																																																																					0	0.378										
CALM1P2	804	bcgsc.ca	37	7	55327599	55327599	+	IGR	SNP	A	A	G	rs7787331	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:55327599A>G								EGFR (3286 upstream) : LANCL2 (105541 downstream)																							TTCTTCATCTATTAGTTTTTC	0.363													G|||	1757	0.350839	0.7239	0.1859	5008	,	,		17825	0.2351		0.1958	False		,,,				2504	0.2423				.													.	.			0			.																																									SO:0001628	intergenic_variant	804	.			TCATCTATTAGTT																													7.37:g.55327599A>G			Somatic	44	0	0		WXS	Illumina HiSeq	Phase_1	40	0.18	7	.	0		0		RNA	SNP		37																																																																																					0	0.363										
FKBP9P1	360132	bcgsc.ca	37	7	55774888	55774888	+	IGR	SNP	C	C	T	rs12666519	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	302	0	0		WXS	Illumina HiSeq	Phase_1	338	0.07	22	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.438										
CCNJP1	100128459	bcgsc.ca	37	7	56296553	56296553	+	IGR	SNP	G	G	T	rs10235373	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296553G>T								NUPR1L (112460 upstream) : AC073136.1 (40922 downstream)																							ACAGCTTGGTGGTTCTGACTA	0.502													T|||	2072	0.413738	0.5696	0.2349	5008	,	,		21593	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			CTTGGTGGTTCTG																													7.37:g.56296553G>T			Somatic	62	0	0		WXS	Illumina HiSeq	Phase_1	78	0.13	10	.	0		0		RNA	SNP		37																																																																																					0	0.502										
CCNJP1	100128459	bcgsc.ca	37	7	56296598	56296598	+	IGR	SNP	A	A	G	rs1640564	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296598A>G								NUPR1L (112505 upstream) : AC073136.1 (40877 downstream)																							TGAGGTGTCTAATGGAGATAT	0.493													G|||	2072	0.413738	0.5696	0.2349	5008	,	,		19994	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			GTGTCTAATGGAG																													7.37:g.56296598A>G			Somatic	81	0	0		WXS	Illumina HiSeq	Phase_1	72	0.10	7	.	0		0		RNA	SNP		37																																																																																					0	0.493										
CCNJP1	100128459	bcgsc.ca	37	7	56296728	56296728	+	IGR	SNP	A	A	G	rs1640565	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296728A>G								NUPR1L (112635 upstream) : AC073136.1 (40747 downstream)																							CATCATTATCATGAGCGATCA	0.473													G|||	2072	0.413738	0.5696	0.2349	5008	,	,		21573	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			ATTATCATGAGCG																													7.37:g.56296728A>G			Somatic	78	0	0		WXS	Illumina HiSeq	Phase_1	89	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.473										
CCNJP1	100128459	bcgsc.ca	37	7	56296746	56296746	+	IGR	SNP	T	T	C	rs1621849	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296746T>C								NUPR1L (112653 upstream) : AC073136.1 (40729 downstream)																							TCAATAGCTGTTCAATACACT	0.453													T|||	2072	0.413738	0.5696	0.2349	5008	,	,		21330	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			TAGCTGTTCAATA																													7.37:g.56296746T>C			Somatic	85	0	0		WXS	Illumina HiSeq	Phase_1	90	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.453										
CCNJP1	100128459	bcgsc.ca	37	7	56296924	56296924	+	IGR	SNP	C	C	T	rs1622932	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296924C>T								NUPR1L (112831 upstream) : AC073136.1 (40551 downstream)																							GTAATCTGCACATTTGGCCAT	0.398													T|||	2072	0.413738	0.5696	0.2349	5008	,	,		19517	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			TCTGCACATTTGG																													7.37:g.56296924C>T			Somatic	59	0	0		WXS	Illumina HiSeq	Phase_1	64	0.17	11	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.398										
CCNJP1	100128459	bcgsc.ca	37	7	56296984	56296984	+	IGR	SNP	C	C	T	rs1640566	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56296984C>T								NUPR1L (112891 upstream) : AC073136.1 (40491 downstream)																							GTCATGAAGACCTGTTTTGTG	0.408													T|||	2072	0.413738	0.5696	0.2349	5008	,	,		18953	0.6111		0.2058	False		,,,				2504	0.3405				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			TGAAGACCTGTTT																													7.37:g.56296984C>T			Somatic	88	0	0		WXS	Illumina HiSeq	Phase_1	92	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.408										
CCNJP1	100128459	bcgsc.ca	37	7	56297387	56297387	+	IGR	SNP	C	C	T	rs1640567	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:56297387C>T								NUPR1L (113294 upstream) : AC073136.1 (40088 downstream)																							CTGGCCTTTACAGGAGGGCAA	0.577													T|||	2072	0.413738	0.5703	0.2349	5008	,	,		17950	0.6111		0.2058	False		,,,				2504	0.3395				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			CCTTTACAGGAGG																													7.37:g.56297387C>T			Somatic	29	0	0		WXS	Illumina HiSeq	Phase_1	39	0.13	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.577										
YWHAEP1	649395	bcgsc.ca	37	7	63894558	63894558	+	IGR	SNP	A	A	C	rs73125103	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:63894558A>C								ZNF736 (79320 upstream) : ZNF680 (85703 downstream)																							TGTACTGGACAAAAACCTCAT	0.403													.|||	516	0.103035	0.0719	0.1167	5008	,	,		19365	0.005		0.1958	False		,,,				2504	0.1411				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGGACAAAAACC																													7.37:g.63894558A>C			Somatic	199	0	0		WXS	Illumina HiSeq	Phase_1	198	0.11	21	.	11	0.00	0		RNA	SNP		37																																																																																					0	0.403										
Unknown	0	bcgsc.ca	37	7	64030116	64030116	+	IGR	SNP	C	C	T	rs1446886	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:64030116C>T								ZNF680 (6632 upstream) : ZNF107 (96459 downstream)																							GCGCAGTAGGCGGCCCGGCCC	0.667													C|||	1097	0.21905	0.2209	0.2219	5008	,	,		15974	0.0833		0.2475	False		,,,				2504	0.3252				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTAGGCGGCCCG																													7.37:g.64030116C>T			Somatic	37	0	0		WXS	Illumina HiSeq	Phase_1	48	0.15	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.667										
Unknown	0	bcgsc.ca	37	7	66038472	66038472	+	IGR	SNP	G	G	A	rs13240501	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:66038472G>A								GS1-124K5.11 (30936 upstream) : KCTD7 (55395 downstream)																							CTTGGAGAATGTGAGGGATTG	0.483													g|||	3135	0.625998	0.7655	0.6398	5008	,	,		19442	0.5526		0.6382	False		,,,				2504	0.4908				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGAATGTGAGGG																													7.37:g.66038472G>A			Somatic	136	0	0		WXS	Illumina HiSeq	Phase_1	168	0.08	14	.	203	0.00	0		RNA	SNP		37																																																																																					0	0.483										
FAM185BP	641808	bcgsc.ca	37	7	76728248	76728248	+	RNA	SNP	C	C	T	rs2539289	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:76728248C>T	ENST00000459742.1	+	0	58																											TTACCCATCTCGCTTTGTAAT	0.318													T|||	1901	0.379593	0.3275	0.3775	5008	,	,		14210	0.4931		0.3718	False		,,,				2504	0.3425				.													.	.			0			.																																											641808	.			CCATCTCGCTTTG																													7.37:g.76728248C>T			Somatic	151	0	0		WXS	Illumina HiSeq	Phase_1	214	0.07	14	.	0		0		RNA	SNP	ENST00000459742.1	37																																																																																						0.318	RP11-467H10.2-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000473089.1			
ZNF804B	219578	bcgsc.ca	37	7	88964226	88964227	+	Missense_Mutation	DNP	CC	CC	AG	rs71526642|rs76870774|rs79931924	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_1	186	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	
DLX6	1750	hgsc.bcm.edu	37	7	96637151	96637151	+	Intron	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:96637151C>T	ENST00000518156.2	+	2	1060				DLX6-AS2_ENST00000606174.1_RNA|DLX6-AS1_ENST00000430404.2_RNA|DLX6-AS1_ENST00000430027.3_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000437541.1_RNA|DLX6_ENST00000493273.2_Intron|DLX6_ENST00000555308.1_Intron|DLX6_ENST00000007660.5_Intron|DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6-AS1_ENST00000605417.1_RNA			P56179	DLX6_HUMAN	distal-less homeobox 6						anatomical structure formation involved in morphogenesis (GO:0048646)|embryonic limb morphogenesis (GO:0030326)|epithelial cell differentiation (GO:0030855)|head development (GO:0060322)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|palate development (GO:0060021)|positive regulation of epithelial cell proliferation (GO:0050679)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1)	12	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					CAGGTAATTCCCGAGAAGCCC	0.522																																					.													.	.			0			.												33.0	32.0	32.0					7																	96637151		1930	4138	6068	SO:0001627	intron_variant	285987	.			TAATTCCCGAGAA		CCDS47647.1, CCDS47647.2	7q21.3	2011-06-20	2005-12-22		ENSG00000006377	ENSG00000006377		"""Homeoboxes / ANTP class : NKL subclass"""	2919	protein-coding gene	gene with protein product		600030	"""distal-less homeo box 6"""			7907794	Standard	NM_005222		Approved		uc022ahu.1	P56179	OTTHUMG00000154201	ENST00000518156.2:c.630+8C>T	7.37:g.96637151C>T			Somatic	55	0	0		WXS	Illumina HiSeq	.	47	0.19	9	.	0		0	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	RNA	SNP	ENST00000518156.2	37	CCDS47647.2																																																																																					0.522	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000334373.4		NM_005222	
AZGP1P1	646282	broad.mit.edu	37	7	99581179	99581179	+	RNA	DEL	C	C	-			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:99581179delC	ENST00000425474.1	+	0	500					NR_036679.1				alpha-2-glycoprotein 1, zinc-binding pseudogene 1																		CCGCATCCCACCCCCCCCACA	0.577																																					.													.	.			0			.																																											0	.			ATCCCACCCCCCC	AW995302		7q22.1	2010-04-16	2006-11-07		ENSG00000214313	ENSG00000214313			911	pseudogene	pseudogene			"""alpha-2-glycoprotein 1, zinc pseudogene 1"""			8241150, 8307568	Standard	NR_036679		Approved		uc003usi.2		OTTHUMG00000156513		7.37:g.99581179delC			Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000425474.1	37																																																																																						0.577	AZGP1P1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000344467.1			
PPP1R2P6	100130972	bcgsc.ca	37	7	139992942	139992942	+	IGR	SNP	A	A	G	rs12703712	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr7:139992942A>G								RNU1-58P (51110 upstream) : SLC37A3 (40609 downstream)																							GCGACAATTTAAAATGAAAAG	0.403													G|||	2440	0.48722	0.2383	0.598	5008	,	,		20406	0.6161		0.4861	False		,,,				2504	0.6135				.													.	.			0			.																																									SO:0001628	intergenic_variant	100130972	.			CAATTTAAAATGA																													7.37:g.139992942A>G			Somatic	33	0	0		WXS	Illumina HiSeq	Phase_1	57	0.11	6	.	0		0		RNA	SNP		37																																																																																					0	0.403										
AC099552.4	0	bcgsc.ca	37	7	154989982	154989982	+	Missense_Mutation	SNP	G	G	A	rs28664023	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	188	0.0053191489	1		WXS	Illumina HiSeq	Phase_1	208	0.05	11	.	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			
Unknown	0	bcgsc.ca	37	8	13880562	13880562	+	IGR	SNP	G	G	T	rs7003822	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	192	0	0		WXS	Illumina HiSeq	Phase_1	187	0.07	13	.	0		0		RNA	SNP		37																																																																																					0	0.383										
Unknown	0	bcgsc.ca	37	8	70042263	70042263	+	IGR	SNP	A	A	G	rs67905920	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	48	0	0		WXS	Illumina HiSeq	Phase_1	55	0.11	6	.	3	0.33	1		RNA	SNP		37																																																																																					0	0.512										
CDK5PS	392265	bcgsc.ca	37	8	123781617	123781617	+	IGR	SNP	G	G	A	rs8192652	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr8:123781617G>A								RP11-973F15.2 (65955 upstream) : RP11-44N11.2 (10592 downstream)																							TGAAATGGGTGAGGCTGGATG	0.502													G|||	418	0.0834665	0.0567	0.1427	5008	,	,		15736	0.0298		0.1511	False		,,,				2504	0.0634				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGGGTGAGGCTG																													8.37:g.123781617G>A			Somatic	23	0	0		WXS	Illumina HiSeq	Phase_1	22	0.27	6	.	0		0		RNA	SNP		37																																																																																					0	0.502										
CDK5PS	392265	bcgsc.ca	37	8	123782133	123782133	+	IGR	SNP	C	C	T	rs6992158	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr8:123782133C>T								RP11-973F15.2 (66471 upstream) : RP11-44N11.2 (10076 downstream)																							CAGGCAATGACGTCGATGACC	0.542													T|||	3186	0.636182	0.7231	0.6052	5008	,	,		21838	0.6617		0.5885	False		,,,				2504	0.5634				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAATGACGTCGAT																													8.37:g.123782133C>T			Somatic	48	0	0		WXS	Illumina HiSeq	Phase_1	46	0.17	8	.	0		0		RNA	SNP		37																																																																																					0	0.542										
LOC101928087	101928087	bcgsc.ca	37	8	143719983	143719983	+	RNA	SNP	G	G	C	rs2280881	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	157	0.0063694268	1		WXS	Illumina HiSeq	Phase_1	177	0.05	9	.	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	66	0	0		WXS	Illumina HiSeq	Phase_1	56	0.07	4	.	1	0.00	0		RNA	SNP	ENST00000413145.1	37																																																																																						0.418	RP11-390F4.6-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000051688.1			
RPL4P5	158345	bcgsc.ca	37	9	7477728	7477728	+	IGR	SNP	T	T	C	rs12683102	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:7477728T>C								KDM4C (302080 upstream) : RP11-77E14.2 (308376 downstream)																							ACGGCGACGGTTTCTCATTTT	0.453													T|||	907	0.18111	0.1346	0.1499	5008	,	,		19875	0.3075		0.1163	False		,,,				2504	0.2025				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGACGGTTTCTCA																													9.37:g.7477728T>C			Somatic	62	0	0		WXS	Illumina HiSeq	Phase_1	49	0.08	4	.	877	0.00	1		RNA	SNP		37																																																																																					0	0.453										
CTAGE12P	392298	bcgsc.ca	37	9	27608549	27608549	+	IGR	SNP	G	G	A	rs142836655	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:27608549G>A								C9orf72 (34685 upstream) : RP11-575I8.1 (220724 downstream)																							ATTTCTCATTGCAAATGGAGC	0.488													G|||	73	0.0145767	0.0045	0.0231	5008	,	,		18326	0.0		0.0437	False		,,,				2504	0.0072				.													.	.			0			.																																									SO:0001628	intergenic_variant	392298	.			CTCATTGCAAATG																													9.37:g.27608549G>A			Somatic	75	0	0		WXS	Illumina HiSeq	Phase_1	59	0.12	7	.	0		0		RNA	SNP		37																																																																																					0	0.488										
RBMXP2	441391	bcgsc.ca	37	9	30689910	30689911	+	IGR	DNP	CA	CA	TG	rs74963277|rs79293599	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:30689910_30689911CA>TG								snoU13 (511335 upstream) : AL590726.2 (81183 downstream)																							TGGTCGTGATCATGACTATTCA	0.45																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			CGTGATCATGACT																													9.37:g.30689910_30689911delinsTG			Somatic	146	0	0		WXS	Illumina HiSeq	Phase_1	110	0.08	9	.	0		0		RNA	DNP		37																																																																																					0	0.450										
Unknown	0	bcgsc.ca	37	9	35147963	35147963	+	IGR	SNP	C	C	T	rs10972346	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:35147963C>T								FAM214B (31625 upstream) : UNC13B (14035 downstream)																							GTGTGAGAACCGGCTAAAGGC	0.388													C|||	2189	0.437101	0.4183	0.6902	5008	,	,		22319	0.2054		0.6054	False		,,,				2504	0.3487				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAGAACCGGCTAA																													9.37:g.35147963C>T			Somatic	657	0.00304414	2		WXS	Illumina HiSeq	Phase_1	452	0.06	25	.	0		0		RNA	SNP		37																																																																																					0	0.388										
Unknown	0	bcgsc.ca	37	9	35147983	35147983	+	IGR	SNP	T	T	C	rs10972347	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:35147983T>C								FAM214B (31645 upstream) : UNC13B (14015 downstream)																							CTTTGCTACATACTTCACATT	0.378													T|||	942	0.188099	0.0507	0.4697	5008	,	,		22116	0.005		0.3867	False		,,,				2504	0.1585				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCTACATACTTCA																													9.37:g.35147983T>C			Somatic	668	0.001497006	1		WXS	Illumina HiSeq	Phase_1	455	0.05	23	.	0		0		RNA	SNP		37																																																																																					0	0.378										
Unknown	0	bcgsc.ca	37	9	35148203	35148203	+	IGR	SNP	C	C	G	rs10972348	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:35148203C>G								FAM214B (31865 upstream) : UNC13B (13795 downstream)																							ATGTGTAGTACTGAGGATTGG	0.388													g|||	2194	0.438099	0.4213	0.6902	5008	,	,		20824	0.2054		0.6064	False		,,,				2504	0.3487				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTAGTACTGAGGA																													9.37:g.35148203C>G			Somatic	142	0	0		WXS	Illumina HiSeq	Phase_1	70	0.10	7	.	0		0		RNA	SNP		37																																																																																					0	0.388										
FAM74A7	100996582	bcgsc.ca;mdanderson.org	37	9	40716224	40716224	+	lincRNA	SNP	C	C	A	rs56989493	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:40716224C>A	ENST00000432614.1	-	0	0				FAM74A3_ENST00000604146.1_lincRNA																							GTTACTGCTGCACTTGGCTGT	0.438																																					.													.	FAM74A3	17		0			.							C		449,3949		9,431,1759	38.0	39.0	39.0			-0.7	0.0	9	dbSNP_134	39	2911,5655		222,2467,1594	no	intergenic				231,2898,3353	AA,AC,CC		33.9832,10.2092,25.9179			40716224	3360,9604	2199	4283	6482			728495	.			CTGCTGCACTTGG																													9.37:g.40716224C>A			Somatic	291	0	0		WXS	Illumina HiSeq	Phase_1	260	0.07	17	.	0		0		RNA	SNP	ENST00000432614.1	37																																																																																						0.438	RP11-395E19.5-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000143688.1			
FAM27E3	100131997	bcgsc.ca	37	9	44998898	44998898	+	IGR	SNP	C	C	T	rs200918750	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:44998898C>T								FAM27C (7415 upstream) : RP11-374M1.5 (3008 downstream)																							cgggagaaaccgcttgtgctt	0.602													c|||	2788	0.556709	0.3427	0.5562	5008	,	,		13779	0.5446		0.7445	False		,,,				2504	0.6656				.													.	.			0			.																																									SO:0001628	intergenic_variant	100287333	.			AGAAACCGCTTGT																													9.37:g.44998898C>T			Somatic	244	0	0		WXS	Illumina HiSeq	Phase_1	259	0.05	13	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.602										
Unknown	0	bcgsc.ca	37	9	76264026	76264026	+	IGR	SNP	C	C	T	rs62540675	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:76264026C>T								RP11-128I7.1 (69612 upstream) : RNA5SP286 (101861 downstream)																							GAAGAAGGGCCTGGAGAATCG	0.527													C|||	79	0.0157748	0.0008	0.0245	5008	,	,		20245	0.0		0.0189	False		,,,				2504	0.0429				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGGGCCTGGAGA																													9.37:g.76264026C>T			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_1	39	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.527										
RP13-60M5.2	0	bcgsc.ca	37	9	91262387	91262387	+	lincRNA	SNP	G	G	A	rs28550932	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:91262387G>A	ENST00000418343.2	-	0	364																											AGCATGTCCCGTGTCTGCCAC	0.433													A|||	1009	0.201478	0.2958	0.2233	5008	,	,		21260	0.1706		0.164	False		,,,				2504	0.1288				p.R86W													.	.			0			c.C256T							A	TRP/ARG	1003,2875		135,733,1071	108.0	110.0	110.0		256	0.2	0.0	9	dbSNP_125	110	1300,6980		97,1106,2937	yes	missense	LOC286238	NM_001100111.1	101	232,1839,4008	AA,AG,GG		15.7005,25.8638,18.9423		86/113	91262387	2303,9855	1939	4140	6079			0	exon2			TGTCCCGTGTCTG																													9.37:g.91262387G>A			Somatic	101	0	0		WXS	Illumina HiSeq	Phase_1	92	0.08	7	NM_001100111	0		0		RNA	SNP	ENST00000418343.2	37																																																																																						0.433	RP13-60M5.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000052976.2			
AUH	549	bcgsc.ca	37	9	94060353	94060353	+	Missense_Mutation	SNP	G	G	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:94060353G>T	ENST00000375731.4	-	5	534	c.511C>A	c.(511-513)Ctt>Att	p.L171I	AUH_ENST00000303617.5_Missense_Mutation_p.L142I|AUH_ENST00000422391.2_Missense_Mutation_p.L171I|AUH_ENST00000478465.1_5'UTR	NM_001698.2	NP_001689.1	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-CoA hydratase	171					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)|methylglutaconyl-CoA hydratase activity (GO:0004490)|mRNA 3'-UTR binding (GO:0003730)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						GGTACTGGAAGATTAGCTGAA	0.328																																					p.L171I													.	AUH	32		0			c.C511A												95.0	90.0	92.0					9																	94060353		2203	4300	6503	SO:0001583	missense	549	exon5			CTGGAAGATTAGC	X79888	CCDS6689.1	9q22	2014-09-17	2010-04-30		ENSG00000148090	ENSG00000148090			890	protein-coding gene	gene with protein product		600529	"""AU RNA-binding protein/enoyl-Coenzyme A hydratase"", ""AU RNA binding protein/enoyl-Coenzyme A hydratase"""			7892223	Standard	NM_001698		Approved		uc004arf.4	Q13825	OTTHUMG00000020207	ENST00000375731.4:c.511C>A	9.37:g.94060353G>T	ENSP00000364883:p.Leu171Ile		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_1	78	0.06	5	NM_001698	80	0.00	0	B1ALV7|B1ALV8|Q8WUE4	Missense_Mutation	SNP	ENST00000375731.4	37	CCDS6689.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012146	0.75046	.	.	ENSG00000148090	ENST00000375731;ENST00000303617;ENST00000422391	T;T;T	0.78816	-1.21;-1.21;-1.21	5.05	5.05	0.67936	Crotonase, core (1);	0.000000	0.85682	D	0.000000	D	0.85396	0.5687	M	0.73372	2.23	0.80722	D	1	P;D;D	0.61080	0.946;0.963;0.989	D;P;D	0.71870	0.956;0.907;0.975	T	0.80750	-0.1243	10	0.08179	T	0.78	.	18.2084	0.89863	0.0:0.0:1.0:0.0	.	171;142;171	B4DYI6;Q13825-2;Q13825	.;.;AUHM_HUMAN	I	171;142;171	ENSP00000364883:L171I;ENSP00000307334:L142I;ENSP00000402026:L171I	ENSP00000307334:L142I	L	-	1	0	AUH	93100174	1.000000	0.71417	0.964000	0.40570	0.797000	0.45037	7.476000	0.81055	2.630000	0.89119	0.591000	0.81541	CTT			0.328	AUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000053032.1			
LINC00587	414319	bcgsc.ca;mdanderson.org	37	9	105405434	105405434	+	lincRNA	SNP	T	T	C	rs10990214	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chr9:105405434T>C	ENST00000374801.3	+	0	289					NR_103830.1		B1AMM8	CI107_HUMAN	long intergenic non-protein coding RNA 587																		ccagaacaactccatcttgaa	0.448													T|||	685	0.136781	0.0446	0.062	5008	,	,		18794	0.376		0.0567	False		,,,				2504	0.1503				.													.	.			0			.																																											414319	.			AACAACTCCATCT	BC038565		9q31.1	2012-10-12	2012-04-11	2012-04-11	ENSG00000204250	ENSG00000204250		"""Long non-coding RNAs"""	31372	non-coding RNA	RNA, long non-coding			"""chromosome 9 open reading frame 107"""	C9orf107			Standard	NR_103830		Approved	bA785H23.1		B1AMM8	OTTHUMG00000020393		9.37:g.105405434T>C			Somatic	51	0	0		WXS	Illumina HiSeq	Phase_1	60	0.13	8	.	0		0		RNA	SNP	ENST00000374801.3	37		299	0.13690476190476192	27	0.054878048780487805	21	0.058011049723756904	211	0.3688811188811189	40	0.052770448548812667	T	0.144	-1.098425	0.01843	.	.	ENSG00000204250	ENST00000374801	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.38243	-0.9670	3	0.87932	D	0	.	.	.	.	rs10990214;rs60178762;rs10990214	.	.	.	P	41	.	ENSP00000363934:L41P	L	+	2	0	C9orf107	104445255	0.028000	0.19301	0.026000	0.17262	0.026000	0.11368	0.213000	0.17521	0.166000	0.19597	0.164000	0.16699	CTC			0.448	LINC00587-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000053460.1			
LAMC3	10319	bcgsc.ca	37	9	133901819	133901820	+	Missense_Mutation	DNP	CC	CC	AG	rs2275136|rs386738954|rs2275137	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CC	CC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_1	163	0.06	9	NM_006059	12	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	43	0	0		WXS	Illumina HiSeq	Phase_1	25	0.20	5	.	0		0		RNA	SNP		37																																																																																					0	0.413										
RP11-706O15.1	0	bcgsc.ca	37	X	3736489	3736489	+	Missense_Mutation	SNP	C	C	T	rs1133336	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:3736489C>T	ENST00000425492.2	-	3	598	c.224G>A	c.(223-225)cGc>cAc	p.R75H	RP11-706O15.1_ENST00000471090.1_5'UTR																							tcaccaacagcgtataagcaa	0.368													t|||	2370	0.627815	0.6384	0.4986	3775	,	,		14765	0.2639		0.498	False		,,,				2504	0.4223				.													.	.			0			.																																									SO:0001583	missense	0	.			CAACAGCGTATAA																												ENST00000425492.2:c.224G>A	X.37:g.3736489C>T	ENSP00000409862:p.Arg75His		Somatic	96	0.0104166667	1		WXS	Illumina HiSeq	Phase_1	103	0.08	8	.	119	0.00	0		Missense_Mutation	SNP	ENST00000425492.2	37		1005	0.6057866184448463	209	0.6920529801324503	121	0.4618320610687023	102	0.21338912133891214	262	0.5038461538461538	c	3.119	-0.180914	0.06380	.	.	ENSG00000205664	ENST00000425492	T	0.55413	0.52	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.41142	-0.9525	4	0.87932	D	0	.	.	.	.	rs1133336;rs3195036;rs5916710;rs7062746;rs17313392;rs17418565;rs62576899	.	.	.	H	75	ENSP00000409862:R75H	ENSP00000409862:R75H	R	-	2	0	RP11-706O15.1	3746489	0.064000	0.20934	0.177000	0.23020	0.175000	0.22909	-1.753000	0.01818	-0.862000	0.04089	-0.885000	0.02943	CGC			0.368	RP11-706O15.1-009	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000144334.1			
VDAC1P2	10064	bcgsc.ca	37	X	49397627	49397627	+	IGR	SNP	T	T	C	rs7891756	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:49397627T>C								GAGE1 (26669 upstream) : PAGE1 (54425 downstream)																							TTAGCATTTTTCCCCCCCAGT	0.488													T|||	1507	0.399205	0.0825	0.2968	3775	,	,		14880	0.2808		0.4652	False		,,,				2504	0.4509				.													.	.			0			.																																									SO:0001628	intergenic_variant	10064	.			CATTTTTCCCCCC																													X.37:g.49397627T>C			Somatic	40	0	0		WXS	Illumina HiSeq	Phase_1	34	0.21	7	.	0		0		RNA	SNP		37																																																																																					0	0.488										
Unknown	0	bcgsc.ca	37	X	61999396	61999396	+	IGR	SNP	A	A	C	rs60576970		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:61999396A>C								None (None upstream) : SPIN4 (567710 downstream)																							CAAAAGAGGGAATAATTCTAA	0.363													.|||	2211	0.585695	0.6982	0.3804	3775	,	,		12551	0.2629		0.3936	False		,,,				2504	0.3712				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGAGGGAATAATT																													X.37:g.61999396A>C			Somatic	29	0	0		WXS	Illumina HiSeq	Phase_1	33	0.12	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.363										
Unknown	0	bcgsc.ca	37	X	65176531	65176531	+	IGR	SNP	T	T	C	rs199968155		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	211	0.0047393365	1		WXS	Illumina HiSeq	Phase_1	282	0.03	9	.	37	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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	208	0	0		WXS	Illumina HiSeq	Phase_1	291	0.03	9	.	27	0.00	0		RNA	SNP		37																																																																																					0	0.507										
TAF1	6872	hgsc.bcm.edu	37	X	70617455	70617455	+	Intron	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:70617455C>T	ENST00000373790.4	+	23	3668				TAF1_ENST00000423759.1_Intron|TAF1_ENST00000449580.1_Intron|TAF1_ENST00000276072.3_Intron	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa						cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				gcctcaacttccagagtagct	0.502																																					.													.	.			0			.																																									SO:0001627	intron_variant	618	.			CAACTTCCAGAGT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3617+139C>T	X.37:g.70617455C>T			Somatic	34	0	0		WXS	Illumina HiSeq	.	42	0.17	7	.	0		0	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	RNA	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																					0.502	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000058995.2		NM_004606	
PRKRIRP1	728748	bcgsc.ca	37	X	73617109	73617109	+	IGR	SNP	C	C	T	rs34974916	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:73617109C>T								RN7SL790P (6287 upstream) : SLC16A2 (23975 downstream)																							CACTTCTATACGTGTCAGCAT	0.433													C|||	1859	0.49245	0.3812	0.5706	3775	,	,		14799	0.0337		0.5338	False		,,,				2504	0.3967				.													.	.			0			.																																									SO:0001628	intergenic_variant	728748	.			TCTATACGTGTCA																													X.37:g.73617109C>T			Somatic	50	0	0		WXS	Illumina HiSeq	Phase_1	55	0.18	10	.	0		0		RNA	SNP		37																																																																																					0	0.433										
KIF4CP	347363	bcgsc.ca	37	X	78580025	78580025	+	IGR	SNP	A	A	C	rs115569657		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:78580025A>C								GPR174 (152299 upstream) : ITM2A (35855 downstream)																							CCAGGAACAAACCTGTTGTTA	0.438													A|||	528	0.139868	0.0272	0.0865	3775	,	,		13677	0.0704		0.1223	False		,,,				2504	0.2434				.													.	.			0			.																																									SO:0001628	intergenic_variant	347363	.			GAACAAACCTGTT																													X.37:g.78580025A>C			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_1	31	0.13	4	.	0		0		RNA	SNP		37																																																																																					0	0.438										
HK2P1	642546	bcgsc.ca	37	X	79827607	79827607	+	IGR	SNP	A	A	G	rs1828209	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:79827607A>G								FAM46D (126797 upstream) : BRWD3 (98745 downstream)																							CCACCACAGCAGCCATGCCTG	0.577													g|||	2616	0.69298	0.5076	0.6311	3775	,	,		13252	0.4623		0.661	False		,,,				2504	0.3845				.													.	.			0			.																																									SO:0001628	intergenic_variant	642546	.			CACAGCAGCCATG																													X.37:g.79827607A>G			Somatic	33	0	0		WXS	Illumina HiSeq	Phase_1	56	0.13	7	.	0		0		RNA	SNP		37																																																																																					0	0.577										
USP12PX	254700	bcgsc.ca	37	X	89367831	89367831	+	IGR	SNP	C	C	T	rs111832781		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	43	0	0		WXS	Illumina HiSeq	Phase_1	34	0.12	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.408										
Unknown	0	bcgsc.ca	37	X	100212432	100212432	+	IGR	SNP	C	C	G	rs12842818	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:100212432C>G								XKRX (28010 upstream) : ARL13A (12267 downstream)																							TAAATGAGGCCTCTCGCTCCC	0.507													c|||	391	0.103576	0.0356	0.0879	3775	,	,		14335	0.0476		0.171	False		,,,				2504	0.0644				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGAGGCCTCTCGC																													X.37:g.100212432C>G			Somatic	74	0	0		WXS	Illumina HiSeq	Phase_1	95	0.13	12	.	0		0		RNA	SNP		37																																																																																					0	0.507										
FRMPD3	84443	broad.mit.edu	37	X	106846478	106846480	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	CAG	CAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:106846478_106846480delCAG	ENST00000276185.4	+	16	5308_5310	c.5308_5310delCAG	c.(5308-5310)cagdel	p.Q1776del				Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	1776	Gln-rich.					cytoskeleton (GO:0005856)				breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(16)|ovary(2)|urinary_tract(1)	28						gcaacaacaacagcagcagcagc	0.586																																					.													.	.			0			.									51,2272		9,27,6,1017,211						0.5	0.8			2	74,3975		18,26,12,1566,817	no	coding	FRMPD3	XM_042978.7		27,53,18,2583,1028	A1A1,A1R,A1,RR,R		1.8276,2.1954,1.9617				125,6247				SO:0001651	inframe_deletion	84443	.			CAACAACAGCAGC	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.5308_5310delCAG	X.37:g.106846487_106846489delCAG	ENSP00000276185:p.Gln1776del		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	127	0.00	0	.	0		0	Q96JK8	In_Frame_Del	DEL	ENST00000276185.4	37																																																																																						0.586	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
API5P1	642812	bcgsc.ca	37	X	115239568	115239568	+	IGR	SNP	G	G	A			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:115239568G>A								RN7SL712P (130468 upstream) : AGTR2 (62406 downstream)																							TTTTTCCTTAGTACCACCTTT	0.443																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	642812	.			TCCTTAGTACCAC																													X.37:g.115239568G>A			Somatic	43	0	0		WXS	Illumina HiSeq	Phase_1	41	0.15	6	.	0		0		RNA	SNP		37																																																																																					0	0.443										
MRRFP1	286423	bcgsc.ca	37	X	122250996	122250996	+	IGR	SNP	G	G	T	rs6648942	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	159	0.0125786164	2		WXS	Illumina HiSeq	Phase_1	237	0.08	19	.	0		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-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	104	0	0		WXS	Illumina HiSeq	Phase_1	121	0.20	24	.	0		0		RNA	SNP		37																																																																																					0	0.358										
SAGE2P	644717	bcgsc.ca	37	X	134814932	134814932	+	IGR	SNP	G	G	T	rs111943338		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	182	0	0		WXS	Illumina HiSeq	Phase_1	206	0.11	22	.	0		0		RNA	SNP		37																																																																																					0	0.418										
Unknown	0	bcgsc.ca	37	X	145701530	145701530	+	IGR	SNP	T	T	G	rs17273448	byFrequency	TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:145701530T>G								RNA5SP517 (192440 upstream) : CXorf51B (189771 downstream)																							AGCTTCTCCCTCTCGATGCTG	0.642													-|||	643	0.170331	0.025	0.0836	3775	,	,		14197	0.1677		0.1928	False		,,,				2504	0.1933				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTCCCTCTCGAT																													X.37:g.145701530T>G			Somatic	38	0	0		WXS	Illumina HiSeq	Phase_1	44	0.18	8	.	3	1.00	3		RNA	SNP		37																																																																																					0	0.642										
Unknown	0	bcgsc.ca	37	X	145701579	145701579	+	IGR	SNP	C	C	T	rs112188715		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:145701579C>T								RNA5SP517 (192489 upstream) : CXorf51B (189722 downstream)																							CCTCCTGCTGCCTGAACAGCT	0.642													-|||	642	0.170066	0.025	0.0836	3775	,	,		13116	0.1667		0.1928	False		,,,				2504	0.1933				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGCTGCCTGAAC																													X.37:g.145701579C>T			Somatic	44	0	0		WXS	Illumina HiSeq	Phase_1	63	0.17	11	.	132	0.00	0		RNA	SNP		37																																																																																					0	0.642										
Unknown	0	bcgsc.ca	37	X	147279972	147279972	+	IGR	SNP	T	T	C	rs142596624		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	31	0	0		WXS	Illumina HiSeq	Phase_1	37	0.14	5	.	0		0		RNA	SNP		37																																																																																					0	0.532										
U82695.9	0	bcgsc.ca;mdanderson.org	37	X	152751497	152751497	+	Missense_Mutation	SNP	G	G	A	rs56165949		TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:152751497G>A	ENST00000428676.1	+	1	184	c.140G>A	c.(139-141)cGc>cAc	p.R47H	HAUS7_ENST00000370210.1_Intron|HAUS7_ENST00000421080.2_Intron																							GCCATCCCACGCGGCCTCCTG	0.682													G|||	210	0.0556291	0.025	0.0548	3775	,	,		12465	0.004		0.0875	False		,,,				2504	0.0481				.													.	.			0			.																																									SO:0001583	missense	0	.			TCCCACGCGGCCT																												ENST00000428676.1:c.140G>A	X.37:g.152751497G>A	ENSP00000398003:p.Arg47His		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_1	49	0.14	7	.	0		0		Missense_Mutation	SNP	ENST00000428676.1	37		98	0.05907172995780591	5	0.010245901639344262	18	0.05113636363636364	0	0.0	47	0.06582633053221289	G	0.330	-0.956429	0.02267	.	.	ENSG00000224963	ENST00000428676	.	.	.	4.03	-0.0249	0.13937	.	.	.	.	.	T	0.06690	0.0171	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39722	-0.9600	3	.	.	.	.	11.4287	0.50027	0.3118:0.0:0.6882:0.0	rs56165949	.	.	.	T	62	.	.	A	+	1	0	U82695.9	152404691	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.135000	0.10420	-0.521000	0.06426	-1.708000	0.00717	GCG			0.682	U82695.9-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000060961.2			
TAZ	6901	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	153648387	153648387	+	Silent	SNP	T	T	C			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	g.chrX:153648387T>C	ENST00000350743.4	+	7	799	c.510T>C	c.(508-510)atT>atC	p.I170I	TAZ_ENST00000369790.4_Silent_p.I156I|TAZ_ENST00000299328.5_Silent_p.I200I|TAZ_ENST00000475699.1_Silent_p.I173I|TAZ_ENST00000351413.4_Silent_p.I186I|TAZ_ENST00000498029.1_3'UTR|TAZ_ENST00000369776.4_Silent_p.I131I	NM_181311.2	NP_851828.1	Q9GZV5	WWTR1_HUMAN	tafazzin	0					cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			lung(1)	1	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCGCCTGATTGCTGAGTGTC	0.637																																					p.I200I													.	.			0			c.T600C												108.0	99.0	102.0					X																	153648387		2203	4300	6503	SO:0001819	synonymous_variant	6901	exon8			CCTGATTGCTGAG	X92762	CCDS14748.1, CCDS14749.1, CCDS14750.1, CCDS35450.1	Xq28	2014-09-17	2008-07-29		ENSG00000102125	ENSG00000102125			11577	protein-coding gene	gene with protein product	"""Barth syndrome"""	300394	"""endocardial fibroelastosis 2"", ""cardiomyopathy, dilated 3A (X-linked)"""	CMD3A, EFE2, EFE		8042670	Standard	NM_000116		Approved	BTHS, XAP-2, G4.5	uc004fkx.3	Q16635	OTTHUMG00000033190	ENST00000350743.4:c.510T>C	X.37:g.153648387T>C			Somatic	149	0	0		WXS	Illumina HiSeq	.	223	0.10	22	NM_000116	38	0.08	3	D3DNH7|Q8N3P2|Q9Y3W6	Silent	SNP	ENST00000350743.4	37	CCDS14749.1																																																																																					0.637	TAZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000080939.1			
MXRA5Y	286544	bcgsc.ca	37	Y	14107272	14107272	+	IGR	SNP	C	C	T			TCGA-W4-A7U2-01A-11D-A435-10	TCGA-W4-A7U2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88f98c12-9f30-4071-861b-f66445d6d122	90d0d153-4618-406d-b803-64cda8a4ba9a	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			Somatic	103	0	0		WXS	Illumina HiSeq	Phase_1	82	0.20	16	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.632										
