#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IGV	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
PERM1	84808	bcgsc.ca	37	1	915450	915450	+	Silent	SNP	G	G	A			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:915450G>A	ENST00000341290.2	-	3	653	c.618C>T	c.(616-618)tcC>tcT	p.S206S	C1orf170_ENST00000433179.2_Silent_p.S226S			Q5SV97	PERM1_HUMAN		320					regulation of transcription, DNA-templated (GO:0006355)|response to muscle activity (GO:0014850)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											ATTGCGGCTCGGAGGCAGGTG	0.597																																					.													.	C1orf170	5		0			.																																									SO:0001819	synonymous_variant	84808	.			CGGCTCGGAGGCA																												ENST00000341290.2:c.618C>T	1.37:g.915450G>A			130	0	0		109	0.07	8	.	0		0	Q6ZVZ7|Q9BRF2|S5G239	Silent	SNP	ENST00000341290.2	37																																																																																						0.597	C1orf170-001	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000097943.2			
C1orf167	284498	bcgsc.ca	37	1	11832311	11832311	+	Silent	SNP	G	G	C	rs10779764	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:11832311G>C	ENST00000433342.1	+	8	2055	c.2055G>C	c.(2053-2055)ctG>ctC	p.L685L	C1orf167_ENST00000484153.1_3'UTR			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	685										central_nervous_system(1)	1						GAGCTTGGCTGTGCAGGTAGG	0.592													G|||	2847	0.56849	0.379	0.7594	5008	,	,		20298	0.7649		0.6272	False		,,,				2504	0.4264				.													.	.			0			.																																									SO:0001819	synonymous_variant	284498	.			TTGGCTGTGCAGG	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.2055G>C	1.37:g.11832311G>C			308	0.0097402597	3		277	0.04	12	.	0		0	Q8NDA9|Q8NDF3	Silent	SNP	ENST00000433342.1	37		1404	0.6428571428571429	206	0.4186991869918699	269	0.7430939226519337	456	0.7972027972027972	473	0.6240105540897097	G	9.526	1.109600	0.20714	.	.	ENSG00000215910	ENST00000312793	.	.	.	3.6	0.23	0.15372	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21256	P	0.999741148	.	.	.	.	.	.	T	0.28459	-1.0043	3	.	.	.	.	10.7852	0.46401	0.0:0.5016:0.4984:0.0	rs10779764	.	.	.	L	45	.	.	V	+	1	0	C1orf167	11754898	0.104000	0.21937	0.944000	0.38274	0.592000	0.36648	0.023000	0.13533	0.306000	0.22856	0.462000	0.41574	GTG			0.592	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca	37	1	11836682	11836682	+	Missense_Mutation	SNP	C	C	T	rs7538516	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:11836682C>T	ENST00000433342.1	+	10	2398	c.2398C>T	c.(2398-2400)Cgc>Tgc	p.R800C	RP11-56N19.5_ENST00000376620.3_RNA|C1orf167_ENST00000484153.1_3'UTR			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	800			R -> C (in dbSNP:rs7538516). {ECO:0000269|PubMed:17974005}.							central_nervous_system(1)	1						GCTTTTCCAGCGCCAGTGGGC	0.672													C|||	2857	0.570487	0.3812	0.7594	5008	,	,		17157	0.7698		0.6252	False		,,,				2504	0.4305				.													.	.			0			.																																									SO:0001583	missense	284498	.			TTCCAGCGCCAGT	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.2398C>T	1.37:g.11836682C>T	ENSP00000414909:p.Arg800Cys		259	0.0038610039	1		221	0.05	12	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		1405|1405	0.6433150183150184|0.6433150183150184	207|207	0.42073170731707316|0.42073170731707316	266|266	0.7348066298342542|0.7348066298342542	459|459	0.8024475524475524|0.8024475524475524	473|473	0.6240105540897097|0.6240105540897097	C|C	9.253|9.253	1.041160|1.041160	0.19669|0.19669	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000312793|ENST00000433342	.|T	.|0.05580	.|3.42	4.65|4.65	0.706|0.706	0.18133|0.18133	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B	.|0.18968	.|0.032	.|B	.|0.15052	.|0.012	T|T	0.04522|0.04522	-1.0945|-1.0945	3|7	.|0.40728	.|T	.|0.16	-5.3817|-5.3817	9.1923|9.1923	0.37207|0.37207	0.0:0.7444:0.0:0.2556|0.0:0.7444:0.0:0.2556	rs7538516;rs7538516|rs7538516;rs7538516	.|800	.|Q5SNV9	.|CA167_HUMAN	V|C	159|800	.|ENSP00000414909:R800C	.|ENSP00000414909:R800C	A|R	+|+	2|1	0|0	C1orf167|C1orf167	11759269|11759269	0.036000|0.036000	0.19791|0.19791	0.078000|0.078000	0.20375|0.20375	0.020000|0.020000	0.10135|0.10135	0.049000|0.049000	0.14099|0.14099	-0.017000|-0.017000	0.14103|0.14103	-1.296000|-1.296000	0.01341|0.01341	GCG|CGC			0.672	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
C1orf167	284498	bcgsc.ca	37	1	11838848	11838848	+	Missense_Mutation	SNP	G	G	T	rs6697244	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:11838848G>T	ENST00000433342.1	+	11	2543	c.2543G>T	c.(2542-2544)aGc>aTc	p.S848I	RP11-56N19.5_ENST00000376620.3_RNA			Q5SNV9	CA167_HUMAN	chromosome 1 open reading frame 167	848			S -> I (in dbSNP:rs6697244). {ECO:0000269|PubMed:17974005}.							central_nervous_system(1)	1						CTGAGCAGCAGCACACTCCAA	0.637													G|||	2858	0.570687	0.3828	0.7594	5008	,	,		14977	0.7698		0.6252	False		,,,				2504	0.4294				.													.	.			0			.																																									SO:0001583	missense	284498	.			GCAGCAGCACACT	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.2543G>T	1.37:g.11838848G>T	ENSP00000414909:p.Ser848Ile		297	0	0		281	0.05	13	.	0		0	Q8NDA9|Q8NDF3	Missense_Mutation	SNP	ENST00000433342.1	37		1405|1405	0.6433150183150184|0.6433150183150184	207|207	0.42073170731707316|0.42073170731707316	266|266	0.7348066298342542|0.7348066298342542	459|459	0.8024475524475524|0.8024475524475524	473|473	0.6240105540897097|0.6240105540897097	G|G	10.25|10.25	1.297401|1.297401	0.23650|0.23650	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000312793|ENST00000433342	.|T	.|0.10192	.|2.9	4.55|4.55	-2.84|-2.84	0.05751|0.05751	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.12630	.|0.006	.|B	.|0.10450	.|0.005	T|T	0.09185|0.09185	-1.0686|-1.0686	4|8	.|0.25106	.|T	.|0.35	-0.0039|-0.0039	6.367|6.367	0.21461|0.21461	0.0:0.1855:0.5088:0.3058|0.0:0.1855:0.5088:0.3058	rs6697244;rs6697244|rs6697244;rs6697244	.|848	.|Q5SNV9	.|CA167_HUMAN	H|I	207|848	.|ENSP00000414909:S848I	.|ENSP00000414909:S848I	Q|S	+|+	3|2	2|0	C1orf167|C1orf167	11761435|11761435	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.080000|0.080000	0.17528|0.17528	-1.006000|-1.006000	0.03671|0.03671	-0.821000|-0.821000	0.04312|0.04312	0.407000|0.407000	0.27541|0.27541	CAG|AGC			0.637	C1orf167-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
MTHFR	4524	bcgsc.ca;mdanderson.org	37	1	11844330	11844330	+	IGR	SNP	C	C	T	rs10864543	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:11844330C>T	ENST00000376592.1	-	0	7057				C1orf167_ENST00000433342.1_Silent_p.A1059A			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)						blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CACTGGGGGCCGTGTTTGCCA	0.662													C|||	2494	0.498003	0.1415	0.7334	5008	,	,		18045	0.7649		0.6173	False		,,,				2504	0.4151				.													.	.			0			.																																									SO:0001628	intergenic_variant	284498	.			GGGGGCCGTGTTT	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277		1.37:g.11844330C>T			196	0	0		158	0.08	13	.	2	0.00	0	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1	1284|1284	0.5879120879120879|0.5879120879120879	101|101	0.20528455284552846|0.20528455284552846	257|257	0.7099447513812155|0.7099447513812155	459|459	0.8024475524475524|0.8024475524475524	467|467	0.6160949868073878|0.6160949868073878	C|C	6.425|6.425	0.446510|0.446510	0.12223|0.12223	.|.	.|.	ENSG00000215910|ENSG00000215910	ENST00000449278|ENST00000312793;ENST00000444493	.|.	.|.	.|.	3.65|3.65	-4.88|-4.88	0.03113|0.03113	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29366|0.29366	-1.0014|-1.0014	3|3	.|.	.|.	.|.	-0.4508|-0.4508	4.8004|4.8004	0.13294|0.13294	0.0:0.2498:0.3001:0.4501|0.0:0.2498:0.3001:0.4501	rs10864543|rs10864543	.|.	.|.	.|.	L|C	145|419;202	.|.	.|.	P|R	+|+	2|1	0|0	C1orf167|C1orf167	11766917|11766917	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.022000|-1.022000	0.03611|0.03611	-0.732000|-0.732000	0.04856|0.04856	-0.254000|-0.254000	0.11334|0.11334	CCG|CGT			0.662	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000006538.1		NM_005957	
PRAMEF30P	441870	bcgsc.ca	37	1	12898512	12898512	+	IGR	SNP	G	G	T	rs116549626	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:12898512G>T								PRAMEF11 (7248 upstream) : HNRNPCL1 (8748 downstream)																							CATTCGTGGAGGTCTCATTTC	0.587													.|||	378	0.0754792	0.0182	0.0159	5008	,	,		17355	0.2282		0.0388	False		,,,				2504	0.0757				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGTGGAGGTCTCA																													1.37:g.12898512G>T			241	0.0082987552	2		155	0.06	10	.	0		0		RNA	SNP		37																																																																																					0	0.587										
PRAMEF30P	441870	bcgsc.ca	37	1	12898517	12898517	+	IGR	SNP	C	C	G	rs72472679	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:12898517C>G								PRAMEF11 (7253 upstream) : HNRNPCL1 (8743 downstream)																							GTGGAGGTCTCATTTCCATGA	0.582																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGTCTCATTTCC																													1.37:g.12898517C>G			227	0	0		157	0.06	10	.	0		0		RNA	SNP		37																																																																																					0	0.582										
PRAMEF30P	441870	bcgsc.ca	37	1	12898551	12898551	+	IGR	SNP	A	A	G	rs117657781	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:12898551A>G								PRAMEF11 (7287 upstream) : HNRNPCL1 (8709 downstream)																							TGAGCTGGGAACAGTGGCTCA	0.577													.|||	377	0.0752796	0.0197	0.0173	5008	,	,		18376	0.2252		0.0378	False		,,,				2504	0.0757				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTGGGAACAGTGG																													1.37:g.12898551A>G			219	0.00456621	1		174	0.06	11	.	0		0		RNA	SNP		37																																																																																					0	0.577										
PRAMEF35P	100419649	bcgsc.ca	37	1	13172124	13172124	+	IGR	SNP	C	C	G	rs61149350	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:13172124C>G								RP13-221M14.3 (7656 upstream) : PRAMEF26 (44231 downstream)																							TGGATACTGTCTGGGTATATC	0.438													.|||	1322	0.263978	0.2753	0.1527	5008	,	,		22429	0.3472		0.1342	False		,,,				2504	0.3753				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TACTGTCTGGGTA																													1.37:g.13172124C>G			624	0.0048076923	3		539	0.09	46	.	0		0		RNA	SNP		37																																																																																					0	0.438										
PRAMEF18	391003	bcgsc.ca;mdanderson.org	37	1	13474974	13474974	+	Silent	SNP	G	G	A	rs201607561	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:13474974G>A	ENST00000376126.2	-	3	1154	c.1155C>T	c.(1153-1155)caC>caT	p.H385H		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	385					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)					lung(2)|ovary(1)	3	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)		TGTCATTGCCGTGAAAGCAGA	0.572													g|||	396	0.0790735	0.0061	0.0173	5008	,	,		15994	0.2659		0.0388	False		,,,				2504	0.0706				p.H385H													.	PRAMEF19	6		0			c.C1155T							G		81,4243		3,75,2084	30.0	33.0	32.0		1155	-1.3	0.0	1	dbSNP_134	32	371,8123		9,353,3885	no	coding-synonymous	PRAMEF18	NM_001099850.1		12,428,5969	AA,AG,GG		4.3678,1.8733,3.5263		385/480	13474974	452,12366	2162	4247	6409	SO:0001819	synonymous_variant	391003	exon3			ATTGCCGTGAAAG			1p36.21	2013-01-17			ENSG00000204491			"""-"""	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.1155C>T	1.37:g.13474974G>A			1083	0	0		930	0.04	40	NM_001099790	0		0		Silent	SNP	ENST00000376126.2	37	CCDS41258.1																																																																																					0.572	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000008177.2		NM_001099850	
Unknown	0	bcgsc.ca	37	1	14507057	14507057	+	IGR	SNP	A	A	G	rs10928050	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:14507057A>G								RNU6-1265P (56227 upstream) : RP11-344F13.1 (41328 downstream)																							GTTCCATGATATTGATGAGGC	0.418													A|||	818	0.163339	0.0514	0.1988	5008	,	,		19699	0.3611		0.1889	False		,,,				2504	0.0593				.													.	.			0			.																																									SO:0001628	intergenic_variant	780789	.			CATGATATTGATG																													1.37:g.14507057A>G			466	0	0		370	0.05	17	.	0		0		Missense_Mutation	SNP		37		440	0.20146520146520147	16	0.032520325203252036	73	0.20165745856353592	213	0.3723776223776224	138	0.1820580474934037	A	10.05	1.243345	0.22796	.	.	ENSG00000218328	ENST00000412667	.	.	.	5.52	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.30179	-0.9987	4	0.45353	T	0.12	-0.4647	3.7651	0.08619	0.1733:0.1929:0.4441:0.1897	rs10928050;rs52831721;rs59509320;rs10928050	.	.	.	M	83	.	ENSP00000412721:I83M	I	+	3	3	C1orf196	14379644	0.000000	0.05858	0.001000	0.08648	0.938000	0.57974	-0.671000	0.05250	-1.746000	0.01335	-0.323000	0.08544	ATA		0	0.418										
FAM46B	115572	bcgsc.ca	37	1	27332465	27332466	+	Missense_Mutation	DNP	GT	GT	AC	rs61737591|rs61737590	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:27332465_27332466GT>AC	ENST00000289166.5	-	2	1412_1413	c.1247_1248AC>GT	c.(1246-1248)cAC>cGT	p.H416R		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	416										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		TGGGATAGGCGTGAGCCAGGAG	0.653																																					p.H416R													.	FAM46B	44		0			c.A1247G																																									SO:0001583	missense	115572	exon2			ATAGGCGTGAGCC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.1247_1248delinsAC	1.37:g.27332465_27332466delinsAC	ENSP00000289166:p.His416Arg		319	0.012539185	4		206	0.08	17	NM_052943	745	0.00	0		Missense_Mutation	DNP	ENST00000289166.5	37	CCDS294.2																																																																																					0.653	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000012347.2		NM_052943	
AK2	204	bcgsc.ca	37	1	59097172	59097172	+	IGR	SNP	C	C	T	rs232916	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:59097172C>T								TACSTD2 (54006 upstream) : MYSM1 (23238 downstream)																							TTAGGACACTCGGGTTCTGCC	0.582													c|||	3296	0.658147	0.8321	0.67	5008	,	,		14446	0.5942		0.5785	False		,,,				2504	0.5624				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GACACTCGGGTTC																													1.37:g.59097172C>T			270	0.0037037037	1		251	0.09	23	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.582										
LINC01359	101927084	bcgsc.ca	37	1	65450611	65450611	+	lincRNA	SNP	C	C	T	rs61734444	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:65450611C>T	ENST00000447748.1	-	0	1775																											AAGAGTTCAGCCACAATAAAC	0.522													C|||	235	0.0469249	0.0356	0.0432	5008	,	,		18593	0.0		0.0487	False		,,,				2504	0.1115				.													.	.			0			.																																											0	.			GTTCAGCCACAAT																													1.37:g.65450611C>T			53	0	0		63	0.08	5	.	0		0		RNA	SNP	ENST00000447748.1	37																																																																																						0.522	RP11-182I10.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000025780.1			
Unknown	0	bcgsc.ca	37	1	85009894	85009894	+	IGR	SNP	A	A	G	rs12143652	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:85009894A>G								SPATA1 (17323 upstream) : CTBS (5394 downstream)														p.K265E(1)									GACAGCTGAAAAAGAGTACAT	0.373													A|||	1181	0.235823	0.2307	0.1614	5008	,	,		18109	0.1984		0.2147	False		,,,				2504	0.3558				.													SPATA1,NS,carcinoma,0,1	.		1	1	Substitution - Missense(1)	prostate(1)	.							A	GLU/LYS	1089,3317	374.6+/-321.3	133,823,1247	144.0	124.0	130.0		793	2.7	0.0	1	dbSNP_120	130	1927,6671	314.9+/-312.0	239,1449,2611	no	missense	SPATA1	XM_003118960.2	56	372,2272,3858	GG,GA,AA		22.4122,24.7163,23.1929	benign	265/407	85009894	3016,9988	2203	4299	6502	SO:0001628	intergenic_variant	100505741	.			GCTGAAAAAGAGT																													1.37:g.85009894A>G			262	0	0		230	0.05	11	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.373										
Unknown	0	bcgsc.ca	37	1	100797449	100797449	+	IGR	SNP	A	A	T	rs614766	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:100797449A>T								RTCA (39124 upstream) : RP5-837M10.2 (12583 downstream)																							AACAAAGGCCATCACGCCATT	0.318													A|||	3134	0.625799	0.9281	0.464	5008	,	,		19780	0.4623		0.5388	False		,,,				2504	0.59				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGGCCATCACGC																													1.37:g.100797449A>T			246	0	0		236	0.05	12	.	0		0		RNA	SNP		37																																																																																					0	0.318										
Unknown	0	bcgsc.ca	37	1	100797473	100797473	+	IGR	SNP	T	T	C	rs614805	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:100797473T>C								RTCA (39148 upstream) : RP5-837M10.2 (12559 downstream)																							TGCTTTGAACTAGAAGAAAAA	0.323													C|||	3190	0.636981	0.966	0.4683	5008	,	,		20517	0.4623		0.5398	False		,,,				2504	0.592				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTGAACTAGAAGA																													1.37:g.100797473T>C			222	0.0135135135	3		211	0.05	11	.	0		0		RNA	SNP		37																																																																																					0	0.323										
NOTCH2NL	388677	broad.mit.edu	37	1	145273262	145273263	+	Frame_Shift_Ins	INS	-	-	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:145273262_145273263insT	ENST00000369340.3	+	4	560_561	c.116_117insT	c.(115-120)acttgtfs	p.C40fs	RP11-458D21.5_ENST00000468030.1_Frame_Shift_Ins_p.C40fs|NOTCH2NL_ENST00000344859.3_Frame_Shift_Ins_p.C40fs|NOTCH2NL_ENST00000362074.6_Frame_Shift_Ins_p.C40fs			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	40	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.T39N(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						AATGGTGGGACTTGTGTGGCCC	0.535																																					p.T39fs													NOTCH2NL_ENST00000362074,caecum,carcinoma,+1,7	NOTCH2NL	100	7	1	Substitution - Missense(1)	ovary(1)	c.116_117insT																																									SO:0001589	frameshift_variant	388677	exon3			GTGGGACTTGTGT		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.118dupT	1.37:g.145273264_145273264dupT	ENSP00000358346:p.Cys40fs		1189	0	0		1319	0.00	6	NM_203458	80	0.00	0	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Frame_Shift_Ins	INS	ENST00000369340.3	37	CCDS909.1																																																																																					0.535	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000038546.1		NM_203458	
RPTN	126638	broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	152127944	152127944	+	Missense_Mutation	SNP	C	C	A			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:152127944C>A	ENST00000316073.3	-	3	1695	c.1631G>T	c.(1630-1632)aGt>aTt	p.S544I		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	544	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						ATAGTGGGAACTCTGGCCTTG	0.512																																					p.S544I													.	RPTN	123		0			c.G1631T												759.0	670.0	697.0					1																	152127944		1568	3582	5150	SO:0001583	missense	126638	exon3			TGGGAACTCTGGC	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1631G>T	1.37:g.152127944C>A	ENSP00000317895:p.Ser544Ile		160	0.00625	1		263	0.08	22	NM_001122965	0		0	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	7.128	0.579248	0.13686	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.13089	2.62	4.05	-5.42	0.02640	.	0.665784	0.12305	U	0.480759	T	0.06962	0.0177	M	0.64567	1.98	0.09310	N	1	D	0.56968	0.978	P	0.53313	0.723	T	0.02617	-1.1133	10	0.34782	T	0.22	-4.2015	3.9271	0.09269	0.3552:0.2944:0.0:0.3505	.	544	Q6XPR3	RPTN_HUMAN	I	544;199	ENSP00000317895:S544I	ENSP00000317895:S544I	S	-	2	0	RPTN	150394568	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.396000	0.02513	-1.047000	0.03242	-0.554000	0.04202	AGT			0.512	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000333867.1		XM_371312	
Unknown	0	bcgsc.ca	37	1	157679691	157679691	+	IGR	SNP	C	C	T	rs17676303	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:157679691C>T								FCRL3 (9044 upstream) : FCRL2 (35831 downstream)																							GGATTGATGCCTGGGCTCAGC	0.473													C|||	788	0.157348	0.062	0.1945	5008	,	,		16245	0.2103		0.2346	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGATGCCTGGGCT																													1.37:g.157679691C>T			263	0.0038022814	1		313	0.10	30	.	49	0.00	0		RNA	SNP		37																																																																																					0	0.473										
Unknown	0	bcgsc.ca	37	1	157679783	157679783	+	IGR	SNP	A	A	G	rs17727309	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:157679783A>G								FCRL3 (9136 upstream) : FCRL2 (35739 downstream)																							ACTGGTGCCCAACCTGGATTA	0.493													A|||	788	0.157348	0.062	0.1945	5008	,	,		19384	0.2103		0.2346	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTGCCCAACCTGG																													1.37:g.157679783A>G			280	0	0		375	0.06	23	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.493										
Unknown	0	bcgsc.ca	37	1	160865612	160865612	+	IGR	SNP	A	A	C	rs112211905	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:160865612A>C								ITLN1 (10652 upstream) : RP11-312J18.6 (35916 downstream)																							AGCTGTTCCAATCTCCACGTC	0.393													-|||	90	0.0179712	0.0053	0.0418	5008	,	,		20868	0.0		0.0497	False		,,,				2504	0.0041				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTTCCAATCTCCA																													1.37:g.160865612A>C			237	0	0		273	0.09	25	.	191	0.00	0		RNA	SNP		37																																																																																					0	0.393										
SLC25A38P1	441915	bcgsc.ca	37	1	172718250	172718250	+	IGR	SNP	C	C	T	rs184779733	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:172718250C>T								FASLG (82236 upstream) : RP1-15D23.2 (26794 downstream)																							TGAGGGGCACCGGGGCCTCTT	0.493													C|||	15	0.00299521	0.0	0.0101	5008	,	,		19370	0.0		0.008	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	441915	.			GGGCACCGGGGCC																													1.37:g.172718250C>T			77	0	0		113	0.04	5	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.493										
SDCCAG3P2	646891	bcgsc.ca	37	1	175013936	175013936	+	IGR	SNP	T	T	A	rs3737935	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:175013936T>A								MRPS14 (21375 upstream) : TNN (23057 downstream)																							GCTTCACCACTGTCAGGCTGG	0.577													T|||	830	0.165735	0.1649	0.0965	5008	,	,		10150	0.3006		0.1342	False		,,,				2504	0.1094				.													.	.			0			.																																									SO:0001628	intergenic_variant	646891	.			CACCACTGTCAGG																													1.37:g.175013936T>A			115	0.0086956522	1		155	0.06	10	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.577										
Unknown	0	bcgsc.ca	37	1	192216349	192216349	+	IGR	SNP	T	T	G	rs139697927	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:192216349T>G								RGS18 (61404 upstream) : RGS21 (69772 downstream)																							TATCTTTTCATGTAGTAACTG	0.393													T|||	5	0.000998403	0.0	0.0014	5008	,	,		21489	0.0		0.004	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTCATGTAGTA																													1.37:g.192216349T>G			353	0.0028328612	1		381	0.05	19	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.393										
Unknown	0	bcgsc.ca	37	1	192216500	192216500	+	IGR	SNP	C	C	A	rs1175146	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:192216500C>A								RGS18 (61555 upstream) : RGS21 (69621 downstream)																							CCATTTTCCCCCAGCATCACC	0.373													C|||	413	0.0824681	0.1641	0.0663	5008	,	,		20989	0.0		0.1024	False		,,,				2504	0.0481				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTCCCCCAGCAT																													1.37:g.192216500C>A			210	0	0		202	0.04	8	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.373										
HHAT	55733	hgsc.bcm.edu;bcgsc.ca	37	1	210577807	210577807	+	Splice_Site	SNP	G	G	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:210577807G>C	ENST00000367010.1	+	6	695		c.e6-1		HHAT_ENST00000545781.1_Splice_Site|HHAT_ENST00000261458.3_Splice_Site|HHAT_ENST00000537898.1_Splice_Site|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000391905.3_Splice_Site|HHAT_ENST00000545154.1_Splice_Site|HHAT_ENST00000308852.6_Splice_Site|HHAT_ENST00000413764.2_Splice_Site	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TGATTTTGTAGAGAAGGTGGT	0.547																																					.													.	.			0			c.469-1G>C												74.0	60.0	65.0					1																	210577807		2203	4300	6503	SO:0001630	splice_region_variant	55733	exon6			TTTGTAGAGAAGG	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.469-1G>C	1.37:g.210577807G>C			116	0	0		94	0.07	7	NM_001122834	0		0	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Splice_Site	SNP	ENST00000367010.1	37	CCDS1495.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354067	0.82243	.	.	ENSG00000054392	ENST00000413764;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1127	0.93323	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	HHAT	208644430	1.000000	0.71417	0.998000	0.56505	0.901000	0.52897	8.717000	0.91425	2.605000	0.88082	0.591000	0.81541	.			0.547	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000088662.1		NM_018194	Intron
LYPLAL1	127018	ucsc.edu	37	1	219347266	219347266	+	Missense_Mutation	SNP	T	T	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:219347266T>C	ENST00000366928.5	+	1	81	c.34T>C	c.(34-36)Tgt>Cgt	p.C12R	LYPLAL1_ENST00000366927.3_Missense_Mutation_p.C12R|RP11-135J2.4_ENST00000441331.1_RNA|LYPLAL1_ENST00000483635.1_3'UTR	NM_138794.3	NP_620149	Q5VWZ2	LYPL1_HUMAN	lysophospholipase-like 1	12					negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|protein depalmitoylation (GO:0002084)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	lysophospholipase activity (GO:0004622)			large_intestine(1)|lung(5)	6				GBM - Glioblastoma multiforme(131;0.055)|all cancers(67;0.105)|OV - Ovarian serous cystadenocarcinoma(81;0.116)		TCTGCAGCGCTGTATCGTGTC	0.617																																					p.C12R													.	LYPLAL1	17		0			c.T34C												67.0	60.0	62.0					1																	219347266		2203	4300	6503	SO:0001583	missense	127018	exon1			CAGCGCTGTATCG	BC016711	CCDS1522.1, CCDS73032.1	1q41	2008-02-05			ENSG00000143353	ENSG00000143353			20440	protein-coding gene	gene with protein product							Standard	XM_005273046		Approved	Q96AV0	uc001hlq.4	Q5VWZ2	OTTHUMG00000037141	ENST00000366928.5:c.34T>C	1.37:g.219347266T>C	ENSP00000355895:p.Cys12Arg		36	0	0		46	0.09	4	NM_138794	93	0.00	0	A8K677|Q5VWZ3|Q7Z4A3|Q96AV0	Missense_Mutation	SNP	ENST00000366928.5	37	CCDS1522.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.196477	0.38806	.	.	ENSG00000143353	ENST00000366928;ENST00000366927	T;T	0.20332	2.08;2.08	4.99	2.53	0.30540	.	0.870811	0.10374	N	0.682473	T	0.35128	0.0921	L	0.47716	1.5	0.23249	N	0.99804	D;D	0.64830	0.988;0.994	P;D	0.67231	0.814;0.95	T	0.12528	-1.0544	10	0.66056	D	0.02	.	7.4745	0.27368	0.348:0.0:0.0:0.652	.	12;12	Q5VWZ2-2;Q5VWZ2	.;LYPL1_HUMAN	R	12	ENSP00000355895:C12R;ENSP00000355894:C12R	ENSP00000355894:C12R	C	+	1	0	LYPLAL1	217413889	0.036000	0.19791	0.004000	0.12327	0.050000	0.14768	1.052000	0.30429	0.409000	0.25649	0.482000	0.46254	TGT			0.617	LYPLAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000090208.1		NM_138794	
OBSCN	84033	ucsc.edu;bcgsc.ca	37	1	228412227	228412228	+	Missense_Mutation	DNP	TG	TG	CA	rs386640006|rs1757153|rs1771480	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	TG	TG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:228412227_228412228TG>CA	ENST00000422127.1	+	9	2765_2766	c.2721_2722TG>CA	c.(2719-2724)agTGcc>agCAcc	p.A908T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A1000T|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A908T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	908	Ig-like 9.		A -> T (in dbSNP:rs1757153).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGGAGCCAGTGCCACACTGAG	0.614																																					p.A908T													.	OBSCN	2142		0			c.G2998A																																									SO:0001583	missense	84033	exon10			AGCCAGTGCCACA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	Exception_encountered	1.37:g.228412227_228412228delinsCA	ENSP00000409493:p.Ala908Thr		127	0.0078740157	1		151	0.11	16	NM_001271223	2	0.00	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	DNP	ENST00000422127.1	37	CCDS58065.1																																																																																					0.614	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding				NM_052843	
Unknown	0	bcgsc.ca	37	1	240136251	240136251	+	IGR	SNP	C	C	G	rs4659558	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:240136251C>G								RP11-35L17.3 (55996 upstream) : FMN2 (118928 downstream)																							ATTGCACTGGCCGACTGGAAG	0.433													G|||	715	0.142772	0.1641	0.1801	5008	,	,		20071	0.1429		0.0447	False		,,,				2504	0.1881				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACTGGCCGACTG																													1.37:g.240136251C>G			48	0	0		42	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.433										
KIF28P	100130097	broad.mit.edu;ucsc.edu	37	1	246939513	246939513	+	RNA	SNP	G	G	A	rs3795467	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:246939513G>A	ENST00000451123.1	-	0	1264				RP11-439E19.3_ENST00000505748.1_RNA|RP11-439E19.3_ENST00000509202.1_RNA|RP11-439E19.3_ENST00000421003.1_RNA|RP11-439E19.10_ENST00000567832.1_RNA																							TGGCAGTTGCGCAGTCATCCC	0.517													g|||	1032	0.20607	0.0885	0.2421	5008	,	,		18282	0.3016		0.2485	False		,,,				2504	0.1973				.													.	.			0			.																																											0	.			AGTTGCGCAGTCA																													1.37:g.246939513G>A			110	0.0090909091	1		109	0.10	11	.	0		0		RNA	SNP	ENST00000451123.1	37																																																																																						0.517	RP11-439E19.8-002	KNOWN	basic|exp_conf	processed_transcript	pseudogene		OTTHUMT00000331247.2			
KIF28P	100130097	bcgsc.ca	37	1	246942159	246942159	+	RNA	SNP	G	G	A	rs7512440	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:246942159G>A	ENST00000451123.1	-	0	775				RP11-439E19.3_ENST00000505748.1_RNA|RP11-439E19.3_ENST00000509202.1_RNA|RP11-439E19.3_ENST00000421003.1_RNA																							TCCAGTTGACGCCAAGGCACC	0.562													G|||	1047	0.209065	0.0991	0.2435	5008	,	,		17719	0.3016		0.2485	False		,,,				2504	0.1973				.													.	.			0			.																																											0	.			GTTGACGCCAAGG																													1.37:g.246942159G>A			137	0.0072992701	1		143	0.06	9	.	0		0		Silent	SNP	ENST00000451123.1	37																																																																																						0.562	RP11-439E19.8-002	KNOWN	basic|exp_conf	processed_transcript	pseudogene		OTTHUMT00000331247.2			
OR2T7	81458	bcgsc.ca	37	1	248605395	248605395	+	Silent	SNP	T	T	G	rs28631666	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr1:248605395T>G	ENST00000460972.3	+	1	888	c.888T>G	c.(886-888)gtT>gtG	p.V296V				P0C7T2	OR2T7_HUMAN	olfactory receptor, family 2, subfamily T, member 7	296						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										AGAAGGTTGTTGGGAGGTGTG	0.453													G|||	1515	0.302516	0.2595	0.2968	5008	,	,		21491	0.4286		0.168	False		,,,				2504	0.3732				.													.	.			0			.																																									SO:0001819	synonymous_variant	81458	.			GGTTGTTGGGAGG			1q44	2013-09-05		2004-03-10	ENSG00000227152	ENSG00000227152		"""GPCR / Class A : Olfactory receptors"""	15019	protein-coding gene	gene with protein product				OR2T7P			Standard	NG_004272		Approved	OST723		P0C7T2	OTTHUMG00000040449	ENST00000460972.3:c.888T>G	1.37:g.248605395T>G			157	0	0		146	0.08	12	.	0		0		RNA	SNP	ENST00000460972.3	37																																																																																						0.453	OR2T7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000097345.3			
SVILP1	645954	bcgsc.ca	37	10	30986348	30986348	+	RNA	SNP	G	G	A	rs4749588	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:30986348G>A	ENST00000435645.1	+	0	338									supervillin pseudogene 1																		CTCGAGCTTCGGCGCTCAATA	0.572													G|||	1205	0.240615	0.0946	0.3329	5008	,	,		18107	0.2599		0.2843	False		,,,				2504	0.3078				.													.	.			0			.																																											0	.			AGCTTCGGCGCTC			10p11.23	2012-12-20			ENSG00000234814	ENSG00000234814			44959	pseudogene	pseudogene							Standard	NR_036438		Approved				OTTHUMG00000017900		10.37:g.30986348G>A			54	0	0		62	0.08	5	.	2	0.00	0		RNA	SNP	ENST00000435645.1	37																																																																																						0.572	SVILP1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331601.1			
EIF3LP2	143341	bcgsc.ca	37	10	43062433	43062433	+	IGR	SNP	G	G	A	rs210224	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:43062433G>A								ZNF37BP (14191 upstream) : ZNF33B (14608 downstream)																							ACAAGATGCTGCGCATGCAGA	0.507													.|||	1461	0.291733	0.0923	0.2522	5008	,	,		16290	0.3899		0.3757	False		,,,				2504	0.4018				.													.	.			0			.																																									SO:0001628	intergenic_variant	143341	.			GATGCTGCGCATG																													10.37:g.43062433G>A			88	0	0		71	0.07	5	.	57	0.00	0		RNA	SNP		37																																																																																					0	0.507										
FAM21C	253725	bcgsc.ca;mdanderson.org	37	10	46245557	46245557	+	Missense_Mutation	SNP	T	T	C	rs112842230	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:46245557T>C	ENST00000336378.4	+	9	864	c.746T>C	c.(745-747)aTg>aCg	p.M249T	FAM21C_ENST00000374362.2_Missense_Mutation_p.M249T|FAM21C_ENST00000359860.4_Missense_Mutation_p.M193T|FAM21C_ENST00000540872.1_Missense_Mutation_p.M249T|FAM21C_ENST00000537517.1_Missense_Mutation_p.M249T	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	249	Glu-rich.				retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						ACCACACAAATGAGTGATGAG	0.388													T|||	606	0.121006	0.0091	0.2594	5008	,	,		13035	0.0327		0.2197	False		,,,				2504	0.1636				p.M249T													.	FAM21C	68		0			c.T746C							T	THR/MET,THR/MET,THR/MET	157,3617		4,149,1734	102.0	97.0	99.0		746,746,746	2.3	0.6	10		99	1634,6566		172,1290,2638	no	missense,missense,missense	FAM21C	NM_001169106.1,NM_001169107.1,NM_015262.2	81,81,81	176,1439,4372	CC,CT,TT		19.9268,4.16,14.9574	benign,benign,benign	249/1280,249/1246,249/1321	46245557	1791,10183	1887	4100	5987	SO:0001583	missense	253725	exon9			CACAAATGAGTGA		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.746T>C	10.37:g.46245557T>C	ENSP00000337541:p.Met249Thr		691	0	0		610	0.04	22	NM_015262	18	0.00	0	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Missense_Mutation	SNP	ENST00000336378.4	37		258	0.11813186813186813	6	0.012195121951219513	84	0.23204419889502761	17	0.02972027972027972	151	0.19920844327176782	T	6.578	0.474930	0.12521	0.0416	0.199268	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000537517;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000420848;ENST00000436993	.	.	.	3.52	2.32	0.28847	.	0.683649	0.16049	N	0.232061	T	0.00012	0.0000	L	0.50333	1.59	0.48571	P	3.269999999999662E-4	B;P;P;P	0.39862	0.372;0.692;0.692;0.646	B;B;B;B	0.42282	0.15;0.275;0.275;0.382	T	0.10268	-1.0637	8	0.23891	T	0.37	-1.2577	8.0543	0.30596	0.0:0.0:0.2066:0.7934	.	249;249;249;194	F5H871;Q9Y4E1-4;Q9Y4E1;Q9Y4E1-3	.;.;FA21C_HUMAN;.	T	249;249;249;249;249;193;194;161	.	ENSP00000337541:M249T	M	+	2	0	FAM21C	45565563	0.998000	0.40836	0.584000	0.28653	0.955000	0.61496	3.670000	0.54569	0.499000	0.27970	0.491000	0.48974	ATG			0.388	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding					
Unknown	0	bcgsc.ca	37	10	79492768	79492768	+	IGR	SNP	T	T	C	rs12782219	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:79492768T>C								KCNMA1 (94415 upstream) : RNU6-1266P (43940 downstream)																							CTGTGGGAGCTGGCACACACA	0.478													C|||	488	0.0974441	0.1513	0.0735	5008	,	,		20925	0.0516		0.1402	False		,,,				2504	0.045				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGGAGCTGGCACA																													10.37:g.79492768T>C			270	0.0037037037	1		193	0.05	10	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.478										
Unknown	0	bcgsc.ca	37	10	79492827	79492827	+	IGR	SNP	C	C	A	rs12780841	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:79492827C>A								KCNMA1 (94474 upstream) : RNU6-1266P (43881 downstream)																							ATATCGGCTCCTTTAAGCATT	0.468													C|||	489	0.0976438	0.152	0.0735	5008	,	,		20132	0.0516		0.1402	False		,,,				2504	0.045				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGGCTCCTTTAAG																													10.37:g.79492827C>A			246	0	0		195	0.05	9	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.468										
Unknown	0	bcgsc.ca	37	10	79492970	79492970	+	IGR	SNP	C	C	T	rs12761718	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:79492970C>T								KCNMA1 (94617 upstream) : RNU6-1266P (43738 downstream)																							GCTGCAGATACACGTGGACAA	0.453													C|||	489	0.0976438	0.1513	0.0735	5008	,	,		23392	0.0526		0.1402	False		,,,				2504	0.045				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGATACACGTGG																													10.37:g.79492970C>T			85	0	0		80	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.453										
BMPR1A	657	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	88676951	88676951	+	Missense_Mutation	SNP	G	G	A			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr10:88676951G>A	ENST00000372037.3	+	9	1273	c.736G>A	c.(736-738)Gga>Aga	p.G246R		NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	246	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.G246R(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						AGGCCGATATGGAGAAGTATG	0.428			"""Mis, N, F"""			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												p.G246R	Ovarian(190;603 2086 22044 30335 47971)		yes	Rec		Juvenile polyposis	10	10q22.3	657	"""bone morphogenetic protein receptor, type IA"""		E	BMPR1A_ENST00000224764,NS,carcinoma,0,2	BMPR1A_ENST00000224764	0	2	2	Substitution - Missense(2)	lung(2)	c.G736A												46.0	44.0	45.0					10																	88676951		2203	4297	6500	SO:0001583	missense	657	exon9	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	CGATATGGAGAAG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"""CD molecules"""	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.736G>A	10.37:g.88676951G>A	ENSP00000361107:p.Gly246Arg		206	0.0048543689	1		232	0.09	21	NM_004329	5	0.20	1	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	37	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	35	5.437054	0.96168	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	T	0.80738	-1.41	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.94814	0.8325	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96554	0.9410	10	0.87932	D	0	.	20.0401	0.97581	0.0:0.0:1.0:0.0	.	246	P36894	BMR1A_HUMAN	R	246	ENSP00000361107:G246R	ENSP00000224764:G246R	G	+	1	0	BMPR1A	88666931	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.869000	0.99810	2.805000	0.96524	0.655000	0.94253	GGA			0.428	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049170.3		NM_004329	
TRIM53CP	340970	bcgsc.ca	37	11	49010832	49010832	+	IGR	SNP	A	A	G	rs10431006	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:49010832A>G								OR4A47 (499500 upstream) : TRIM49B (39671 downstream)																							CTTTTTCAGCATGTGCAAATT	0.373													.|||	645	0.128794	0.003	0.147	5008	,	,		19372	0.1915		0.0875	False		,,,				2504	0.2638				.													.	.			0			.																																									SO:0001628	intergenic_variant	340970	.			TTCAGCATGTGCA																													11.37:g.49010832A>G			834	0.0011990408	1		623	0.04	23	.	0		0		RNA	SNP		37																																																																																					0	0.373										
Unknown	0	bcgsc.ca	37	11	49329521	49329521	+	IGR	SNP	T	T	C	rs1164671	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:49329521T>C								FOLH1 (99299 upstream) : CTD-2026G22.1 (58101 downstream)																							ATTTTGGTCATAAGTCATCCC	0.428													T|||	1043	0.208267	0.09	0.196	5008	,	,		15218	0.2639		0.1899	False		,,,				2504	0.3384				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGGTCATAAGTCA																													11.37:g.49329521T>C			199	0.0050251256	1		209	0.05	10	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.428										
OR4D8P	401696	bcgsc.ca	37	11	59259846	59259846	+	IGR	SNP	C	C	T	rs3862659	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:59259846C>T								OR4D10 (13977 upstream) : RNU6-779P (6618 downstream)																							TCCACCTGCACCTCCCACATC	0.527													C|||	880	0.175719	0.0098	0.33	5008	,	,		18691	0.2351		0.2008	False		,,,				2504	0.2035				.													.	.			0			.																																									SO:0001628	intergenic_variant	401696	.			CCTGCACCTCCCA																													11.37:g.59259846C>T			81	0	0		85	0.06	5	.	0		0		RNA	SNP		37																																																																																					0	0.527										
Unknown	0	bcgsc.ca	37	11	62815424	62815424	+	IGR	SNP	C	C	T	rs7126542	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:62815424C>T								SLC22A8 (32113 upstream) : SLC22A24 (31987 downstream)																							TGGGCCTGCCCGGGCCACAAG	0.592													T|||	1904	0.380192	0.1528	0.4323	5008	,	,		19277	0.506		0.4215	False		,,,				2504	0.4785				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTGCCCGGGCCA																													11.37:g.62815424C>T			49	0	0		39	0.13	5	.	0		0		RNA	SNP		37																																																																																					0	0.592										
INTS4	92105	broad.mit.edu	37	11	77635831	77635832	+	Frame_Shift_Ins	INS	-	-	A			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:77635831_77635832insA	ENST00000534064.1	-	12	1512_1513	c.1478_1479insT	c.(1477-1479)ttafs	p.L493fs	INTS4_ENST00000529807.1_Frame_Shift_Ins_p.L493fs|INTS4_ENST00000525931.1_5'UTR	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	493					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GGTACTTGGTTAAATTTTTCAG	0.391																																					p.L493fs													.	INTS4	89		0			c.1479_1480insT																																									SO:0001589	frameshift_variant	92105	exon12			CTTGGTTAAATTT	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1479dupT	11.37:g.77635834_77635834dupA	ENSP00000434466:p.Leu493fs		603	0	0		395	0.02	6	NM_033547	19	0.00	0	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Frame_Shift_Ins	INS	ENST00000534064.1	37	CCDS31644.1																																																																																					0.391	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390927.1		NM_033547	
ARHGAP42	143872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	100814536	100814536	+	Missense_Mutation	SNP	G	G	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:100814536G>C	ENST00000298815.8	+	10	983	c.980G>C	c.(979-981)tGt>tCt	p.C327S	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.C293S	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	327	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTAAAATCTTGTATCCGACGA	0.333																																					p.C327S													.	.			0			c.G980C												121.0	99.0	105.0					11																	100814536		692	1590	2282	SO:0001583	missense	143872	exon10			AATCTTGTATCCG			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.980G>C	11.37:g.100814536G>C	ENSP00000298815:p.Cys327Ser		123	0	0		74	0.19	14	NM_152432	15	0.87	13	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		.	.	.	.	.	.	.	.	.	.	G	26.3	4.728049	0.89390	.	.	ENSG00000165895	ENST00000524892;ENST00000298815;ENST00000531183	T;T;T	0.50001	0.76;0.76;0.76	5.33	5.33	0.75918	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000008	T	0.74053	0.3666	M	0.90019	3.08	0.80722	D	1	D	0.62365	0.991	D	0.63597	0.916	T	0.80482	-0.1363	10	0.87932	D	0	.	18.6336	0.91369	0.0:0.0:1.0:0.0	.	327	A6NI28	RHG42_HUMAN	S	293;327;183	ENSP00000431776:C293S;ENSP00000298815:C327S;ENSP00000434304:C183S	ENSP00000298815:C327S	C	+	2	0	ARHGAP42	100319746	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.283000	0.95860	2.470000	0.83445	0.563000	0.77884	TGT			0.333	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				NM_152432	
NCAM1	4684	hgsc.bcm.edu	37	11	113078059	113078059	+	Silent	SNP	C	C	T	rs376337341		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr11:113078059C>T	ENST00000533760.1	+	6	950	c.351C>T	c.(349-351)tgC>tgT	p.C117C	NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Silent_p.C234C|NCAM1_ENST00000316851.7_Silent_p.C225C	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	235	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		CCCTGGTGTGCGATGCCGAAG	0.532																																					p.C235C													NCAM1_ENST00000401611,NS,carcinoma,0,3	NCAM1_ENST00000401611	0	3	0			c.C705T							C	,,,,	0,4056		0,0,2028	86.0	87.0	87.0		706,706,706,706,706	-8.0	0.5	11		87	1,8325		0,1,4162	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCAM1	NM_000615.6,NM_001076682.3,NM_001242607.1,NM_001242608.1,NM_181351.4	,,,,	0,1,6190	TT,TC,CC		0.012,0.0,0.0081	,,,,	235/849,235/762,235/885,235/727,235/859	113078059	1,12381	2028	4163	6191	SO:0001819	synonymous_variant	4684	exon7			GGTGTGCGATGCC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.351C>T	11.37:g.113078059C>T			82	0	0		69	0.06	4	NM_001242608	0		0	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Silent	SNP	ENST00000533760.1	37																																																																																						0.532	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000394068.2		NM_000615	
AKAP3	10566	bcgsc.ca	37	12	4735968	4735969	+	Missense_Mutation	DNP	AG	AG	CA	rs71441828|rs67512580|rs2041292|rs2041291	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AG	AG					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:4735968_4735969AG>CA	ENST00000545990.2	-	5	2623_2624	c.2099_2100CT>TG	c.(2098-2100)tCT>tTG	p.S700L	AKAP3_ENST00000228850.1_Missense_Mutation_p.S700L|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	700			S -> F (in dbSNP:rs2041291).|S -> P (in dbSNP:rs2041290).	S -> L (in Ref. 2; AAC35854). {ECO:0000305}.	acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TGGCATCTCCAGACTTGTCATC	0.505																																					p.S700L													.	AKAP3	212		0			c.C2099T																																									SO:0001583	missense	10566	exon4			ATCTCCAGACTTG	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2099_2100delinsCA	12.37:g.4735968_4735969delinsCA	ENSP00000440994:p.Ser700Leu		122	0	0		175	0.05	8	NM_006422	9	0.00	0	O75945|Q86X01|Q9UM61	Missense_Mutation	DNP	ENST00000545990.2	37	CCDS8531.1																																																																																					0.505	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000398911.2		NM_006422	
ANO2	57101	broad.mit.edu	37	12	5841706	5841707	+	Frame_Shift_Ins	INS	-	-	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:5841706_5841707insG	ENST00000356134.5	-	16	1598_1599	c.1527_1528insC	c.(1525-1530)aacacgfs	p.T510fs	ANO2_ENST00000327087.8_Frame_Shift_Ins_p.T509fs|ANO2_ENST00000546188.1_Frame_Shift_Ins_p.T510fs|ANO2_ENST00000538154.1_5'UTR	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	514					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CACTCCGTCGTGTTTGTTTCCA	0.46																																					p.T509fs													.	ANO2	309		0			c.1525_1526insC																																									SO:0001589	frameshift_variant	57101	exon15			CCGTCGTGTTTGT	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1528dupC	12.37:g.5841707_5841707dupG	ENSP00000348453:p.Thr510fs		91	0	0		139	0.05	7	NM_020373	6	0.00	0	C4N787|Q9H847	Frame_Shift_Ins	INS	ENST00000356134.5	37																																																																																						0.460	ANO2-001	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000399019.4		NM_020373	
Unknown	0	bcgsc.ca	37	12	6587668	6587668	+	IGR	SNP	C	C	G	rs7301945	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:6587668C>G								VAMP1 (7515 upstream) : MRPL51 (13481 downstream)																							GAGGGCAGGGCTCACCGTCGG	0.677													C|||	1397	0.278954	0.2799	0.2565	5008	,	,		14941	0.4544		0.1879	False		,,,				2504	0.2065				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCAGGGCTCACCG																													12.37:g.6587668C>G			33	0.0303030303	1		60	0.17	10	.	2	0.00	0		RNA	SNP		37																																																																																					0	0.677										
NIFKP3	100270648	bcgsc.ca	37	12	7757084	7757084	+	IGR	SNP	T	T	C	rs11054742|rs111256632		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:7757084T>C								CD163 (100595 upstream) : APOBEC1 (44911 downstream)																							TTCAGATTTTTGTCTCTCCAA	0.383													t|||	664	0.132588	0.2073	0.281	5008	,	,		-128	0.001		0.1044	False		,,,				2504	0.091				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GATTTTTGTCTCT																													12.37:g.7757084T>C			30	0	0		43	0.21	9	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.383										
CPNE8	144402	broad.mit.edu	37	12	39118673	39118673	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:39118673delT	ENST00000331366.5	-	12	923	c.827delA	c.(826-828)aagfs	p.K278fs	CPNE8_ENST00000360449.3_Frame_Shift_Del_p.K266fs	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	278						extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				ATATTTTTTCTTTTTTCCTTT	0.224																																					p.K276fs													.	CPNE8	66		0			c.827delA												35.0	42.0	40.0					12																	39118673		2084	4232	6316	SO:0001589	frameshift_variant	144402	exon12			TTTTTCTTTTTTC	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.827delA	12.37:g.39118673delT	ENSP00000329748:p.Lys278fs		1160	0	0		1131	0.01	7	NM_153634	2	0.00	0	Q2TB41|Q86VY2	Frame_Shift_Del	DEL	ENST00000331366.5	37	CCDS8733.1																																																																																					0.224	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000403856.1		NM_153634	
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40821867	40821867	+	Missense_Mutation	SNP	G	G	A	rs7958987	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40821867G>A	ENST00000454784.4	+	13	1349	c.616G>A	c.(616-618)Gtc>Atc	p.V206I	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	206			V -> I (in dbSNP:rs7958987).		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						GCCAGGAGAAGTCCGAGAAGG	0.363													G|||	1568	0.313099	0.236	0.2608	5008	,	,		17735	0.3462		0.328	False		,,,				2504	0.4049				.													.	.			0			.																																									SO:0001583	missense	283463	.			GGAGAAGTCCGAG	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.616G>A	12.37:g.40821867G>A	ENSP00000476404:p.Val206Ile		229	0.0131004367	3		251	0.06	15	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		657	0.3008241758241758	113	0.22967479674796748	98	0.27071823204419887	195	0.3409090909090909	251	0.3311345646437995	G	6.280	0.419830	0.11928	.	.	ENSG00000205592	ENST00000425730	.	.	.	5.89	3.1	0.35709	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	0.26556	P	0.9738136	.	.	.	.	.	.	T	0.33317	-0.9873	5	0.19147	T	0.46	.	8.0358	0.30491	0.3793:0.0:0.6207:0.0	rs7958987;rs17467277;rs17492264;rs17527567;rs52791408;rs7958987	.	.	.	I	435	.	ENSP00000395253:V435I	V	+	1	0	MUC19	39108134	0.910000	0.30920	0.792000	0.32020	0.022000	0.10575	0.474000	0.22148	0.407000	0.25591	-0.229000	0.12294	GTC			0.363	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40832126	40832126	+	Silent	SNP	C	C	T	rs10878584	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40832126C>T	ENST00000454784.4	+	21	2398	c.1665C>T	c.(1663-1665)aaC>aaT	p.N555N	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	555					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						GTTACATAAACGACGAGGTCA	0.398													T|||	2595	0.518171	0.3601	0.5648	5008	,	,		19939	0.4742		0.5447	False		,,,				2504	0.7168				.													.	.			0			.																																									SO:0001819	synonymous_variant	283463	.			CATAAACGACGAG	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.1665C>T	12.37:g.40832126C>T			104	0	0		107	0.07	8	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.398	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40834376	40834376	+	Splice_Site	SNP	C	C	G	rs10878592	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40834376C>G	ENST00000454784.4	+	22	2449	c.1716C>G	c.(1714-1716)tgC>tgG	p.C572W	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	572					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						TTATTTCCAGCGTCTGTCGGG	0.343													C|||	2594	0.517971	0.3601	0.5648	5008	,	,		19095	0.4742		0.5447	False		,,,				2504	0.7157				.													.	.			0			.																																									SO:0001630	splice_region_variant	283463	.			TTCCAGCGTCTGT	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.1716-1C>G	12.37:g.40834376C>G			508	0.0019685039	1		494	0.07	35	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1086	0.49725274725274726	198	0.4024390243902439	215	0.5939226519337016	247	0.4318181818181818	426	0.5620052770448549	C	12.41	1.930900	0.34096	.	.	ENSG00000205592	ENST00000425730	.	.	.	5.44	0.143	0.14820	.	.	.	.	.	T	0.00012	0.0000	M	0.90814	3.15	0.09310	P	0.9999999999658039	.	.	.	.	.	.	T	0.43702	-0.9375	4	.	.	.	.	5.5996	0.17347	0.0:0.3108:0.1367:0.5525	rs10878592;rs17445029;rs17521264;rs52833400;rs10878592	.	.	.	W	801	.	.	C	+	3	2	MUC19	39120643	0.983000	0.35010	0.976000	0.42696	0.471000	0.32888	0.078000	0.14761	-0.209000	0.10156	-1.068000	0.02270	TGC			0.343	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	Missense_Mutation
MUC19	283463	bcgsc.ca;mdanderson.org	37	12	40835734	40835734	+	Missense_Mutation	SNP	C	C	G	rs7966110	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40835734C>G	ENST00000454784.4	+	25	2815	c.2082C>G	c.(2080-2082)atC>atG	p.I694M	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	694	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		I -> M (in dbSNP:rs7966110).		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						TCTGCCACATCTATGGGGAAG	0.368													C|||	2596	0.518371	0.3601	0.5663	5008	,	,		16912	0.4742		0.5447	False		,,,				2504	0.7168				.													.	.			0			.																																									SO:0001583	missense	283463	.			CCACATCTATGGG	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.2082C>G	12.37:g.40835734C>G	ENSP00000476404:p.Ile694Met		285	0	0		229	0.08	18	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1086	0.49725274725274726	198	0.4024390243902439	215	0.5939226519337016	247	0.4318181818181818	426	0.5620052770448549	C	15.04	2.715889	0.48622	.	.	ENSG00000205592	ENST00000425730	.	.	.	4.95	3.09	0.35607	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.09310	P	0.999999999999998	.	.	.	.	.	.	T	0.49234	-0.8961	5	0.72032	D	0.01	.	8.9957	0.36050	0.0:0.7499:0.0:0.2501	rs7966110;rs17445043;rs52818908;rs7966110	.	.	.	M	923	.	ENSP00000395253:I923M	I	+	3	3	MUC19	39122001	0.303000	0.24463	1.000000	0.80357	0.976000	0.68499	-0.406000	0.07187	1.210000	0.43336	-0.439000	0.05793	ATC			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	40838216	40838216	+	Missense_Mutation	SNP	T	T	C	rs10784621	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40838216T>C	ENST00000454784.4	+	29	3459	c.2726T>C	c.(2725-2727)gTg>gCg	p.V909A	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	909			V -> A (in dbSNP:rs10784621).		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						TACCATGATGTGTGCATTGAA	0.522													C|||	2596	0.518371	0.3601	0.5663	5008	,	,		20653	0.4752		0.5437	False		,,,				2504	0.7168				.													.	.			0			.																																									SO:0001583	missense	283463	.			ATGATGTGTGCAT	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.2726T>C	12.37:g.40838216T>C	ENSP00000476404:p.Val909Ala		213	0	0		201	0.06	13	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1086	0.49725274725274726	198	0.4024390243902439	215	0.5939226519337016	247	0.4318181818181818	426	0.5620052770448549	C	0.014	-1.599815	0.00849	.	.	ENSG00000205592	ENST00000425730	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	T	0.00012	0.0000	N	0.00027	-2.645	0.09310	P	0.999999999705199	.	.	.	.	.	.	T	0.42632	-0.9440	5	0.06891	T	0.86	.	12.7281	0.57183	0.0:0.9163:0.0:0.0837	rs10784621;rs17467452;rs17497471;rs17521303;rs17588949;rs52806025;rs56659161;rs10784621	.	.	.	A	1138	.	ENSP00000395253:V1138A	V	+	2	0	MUC19	39124483	0.929000	0.31497	0.033000	0.17914	0.003000	0.03518	2.275000	0.43399	1.302000	0.44855	-0.119000	0.15052	GTG			0.522	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40840325	40840325	+	Silent	SNP	T	T	C	rs10878597	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40840325T>C	ENST00000454784.4	+	31	3752	c.3019T>C	c.(3019-3021)Ttg>Ctg	p.L1007L	RP11-115F18.1_ENST00000552757.1_RNA			Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	1007	Approximate repeats of G-V-T-G-T-T-G-P-S- A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(2)	2						TGCTCCTTACTTGGATGAGAA	0.373													C|||	2596	0.518371	0.3601	0.5663	5008	,	,		14910	0.4742		0.5447	False		,,,				2504	0.7168				.													.	.			0			.																																									SO:0001819	synonymous_variant	283463	.			CCTTACTTGGATG	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.3019T>C	12.37:g.40840325T>C			231	0.0043290043	1		195	0.05	10	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.373	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40857943	40857943	+	Missense_Mutation	SNP	A	A	C	rs2933353	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40857943A>C	ENST00000454784.4	+	40	4266	c.3533A>C	c.(3532-3534)gAa>gCa	p.E1178A				Q7Z5P9	MUC19_HUMAN	mucin 19, oligomeric	1178	Approximate repeats of G-V-T-G-T-T-G-P-S- A.		E -> A (in dbSNP:rs2933353).		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						GTATCTGGAGAAACCCCTGCA	0.433													C|||	3466	0.692093	0.5219	0.7622	5008	,	,		17398	0.6607		0.7475	False		,,,				2504	0.8476				.													.	.			0			.																																									SO:0001583	missense	283463	.			CTGGAGAAACCCC	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.3533A>C	12.37:g.40857943A>C	ENSP00000476404:p.Glu1178Ala		113	0	0		137	0.04	5	.	0		0	Q8NA85	Missense_Mutation	SNP	ENST00000454784.4	37		1503	0.6881868131868132	285	0.5792682926829268	273	0.7541436464088398	377	0.6590909090909091	568	0.7493403693931399	C	0.026	-1.368558	0.01225	.	.	ENSG00000205592	ENST00000425730	.	.	.	2.4	0.529	0.17095	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.36383	-0.9750	5	0.08381	T	0.77	.	2.5809	0.04818	0.2259:0.4978:0.0:0.2763	rs2933353;rs52795487;rs2933353	.	.	.	A	1407	.	ENSP00000395253:E1407A	E	+	2	0	MUC19	39144210	0.000000	0.05858	0.002000	0.10522	0.029000	0.11900	-1.103000	0.03329	-0.151000	0.11176	-0.709000	0.03644	GAA			0.433	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40951596	40951596	+	Intron	SNP	A	A	G	rs3751167	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40951596A>G	ENST00000454784.4	+	70	18503							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						CATCTTTTCCACTTTTCTTGA	0.318													A|||	788	0.157348	0.2065	0.1484	5008	,	,		18058	0.1706		0.161	False		,,,				2504	0.0798				.													.	.			0			.																																									SO:0001627	intron_variant	283463	.			TTTTCCACTTTTC	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.10890+277A>G	12.37:g.40951596A>G			208	0	0		198	0.07	14	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.318	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
MUC19	283463	bcgsc.ca	37	12	40951605	40951605	+	Intron	SNP	G	G	A	rs3751168	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:40951605G>A	ENST00000454784.4	+	70	18503							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						CACTTTTCTTGATTTGCTCTT	0.323													A|||	997	0.199081	0.3585	0.1571	5008	,	,		17969	0.1706		0.163	False		,,,				2504	0.0798				.													.	.			0			.																																									SO:0001627	intron_variant	283463	.			TTTCTTGATTTGC	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.10890+286G>A	12.37:g.40951605G>A			211	0.0047393365	1		209	0.07	14	.	0		0	Q8NA85	Silent	SNP	ENST00000454784.4	37																																																																																						0.323	MUC19-001	NOVEL	non_canonical_conserved|non_canonical_genome_sequence_error|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000384257.6		XM_003403524	
Unknown	0	bcgsc.ca	37	12	43965108	43965108	+	IGR	SNP	T	T	A	rs11611126	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:43965108T>A								ADAMTS20 (19384 upstream) : RP11-350F4.2 (147687 downstream)																							TCTTCTCCAATACAGTTCTCA	0.433													T|||	802	0.160144	0.0204	0.2651	5008	,	,		20799	0.2768		0.1352	False		,,,				2504	0.18				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCCAATACAGTT																													12.37:g.43965108T>A			148	0.0202702703	3		137	0.06	8	.	0		0		RNA	SNP		37																																																																																					0	0.433										
DYRK2	8445	hgsc.bcm.edu	37	12	68051843	68051844	+	Frame_Shift_Ins	INS	-	-	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:68051843_68051844insG	ENST00000344096.3	+	3	1569_1570	c.1156_1157insG	c.(1156-1158)cgtfs	p.R386fs	DYRK2_ENST00000393555.3_Frame_Shift_Ins_p.R313fs|RP11-335O4.3_ENST00000425371.2_RNA	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	386	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CATCCAGTCGCGTTTTTACCGG	0.49																																					p.R386fs													DYRK2,NS,carcinoma,0,1	DYRK2	63		0			c.1156_1157insG																																									SO:0001589	frameshift_variant	8445	exon3			CAGTCGCGTTTTT	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1157dupG	12.37:g.68051844_68051844dupG	ENSP00000342105:p.Arg386fs		114	0	0		131	0.08	11	NM_006482	34	0.00	0	B2R9V9|Q9BRB5	Frame_Shift_Ins	INS	ENST00000344096.3	37	CCDS8978.1																																																																																					0.490	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000402218.1			
BEST3	144453	bcgsc.ca;mdanderson.org	37	12	70037520	70037520	+	Missense_Mutation	SNP	G	G	A	rs61747221	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:70037520G>A	ENST00000331471.4	-	10	1319	c.1148C>T	c.(1147-1149)cCa>cTa	p.P383L		NM_001282614.1	NP_001269543.1	Q8N1M1	BEST3_HUMAN	bestrophin 3	0					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			ctgagggagtgggatttttat	0.443													G|||	691	0.137979	0.1694	0.062	5008	,	,		21522	0.2341		0.0875	False		,,,				2504	0.1022				.													.	.			0			.																																									SO:0001583	missense	144453	.			GGGAGTGGGATTT	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000331471.4:c.1148C>T	12.37:g.70037520G>A	ENSP00000329064:p.Pro383Leu		243	0	0		200	0.07	13	.	0		0	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Missense_Mutation	SNP	ENST00000331471.4	37		318	0.14560439560439561	81	0.16463414634146342	29	0.08011049723756906	140	0.24475524475524477	68	0.08970976253298153	G	9.433	1.086090	0.20390	.	.	ENSG00000127325	ENST00000331471	D	0.98192	-4.78	3.74	-0.249	0.13011	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.80722	P	0.0	B	0.19583	0.037	B	0.20955	0.032	T	0.54384	-0.8302	7	0.48119	T	0.1	.	3.8985	0.09150	0.3062:0.1853:0.5085:0.0	.	383	Q8N1M1-1	.	L	383	ENSP00000329064:P383L	ENSP00000329064:P383L	P	-	2	0	BEST3	68323787	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.112000	0.15479	-0.057000	0.13199	-0.137000	0.14449	CCA			0.443	BEST3-008	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000403865.1		NM_152439	
TRAFD1	10906	broad.mit.edu	37	12	112589651	112589652	+	Frame_Shift_Ins	INS	-	-	A	rs16934188		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:112589651_112589652insA	ENST00000257604.5	+	10	1943_1944	c.1326_1327insA	c.(1327-1329)aatfs	p.N443fs	TRAFD1_ENST00000412615.2_Frame_Shift_Ins_p.N443fs|Y_RNA_ENST00000363265.1_RNA	NM_001143906.1	NP_001137378.1	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	443					negative regulation of innate immune response (GO:0045824)|response to cytokine (GO:0034097)		metal ion binding (GO:0046872)			kidney(5)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	17						AGGAAACAGCTAATGGGCCCAC	0.495																																					p.A442fs													.	TRAFD1	42		0			c.1326_1327insA																																									SO:0001589	frameshift_variant	10906	exon10			AACAGCTAATGGG	AB007447	CCDS9160.1	12q24.13	2013-01-25			ENSG00000135148	ENSG00000135148			24808	protein-coding gene	gene with protein product		613197				12477932	Standard	NM_006700		Approved	FLN29	uc001ttp.3	O14545	OTTHUMG00000169640	ENST00000257604.5:c.1328dupA	12.37:g.112589653_112589653dupA	ENSP00000257604:p.Asn443fs		364	0	0		385	0.02	6	NM_001143906	113	0.00	0	A8K5L6|B4DI89	Frame_Shift_Ins	INS	ENST00000257604.5	37	CCDS9160.1																																																																																					0.495	TRAFD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000405214.1		NM_006700	
NCOR2	9612	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	124887093	124887093	+	Silent	SNP	C	C	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr12:124887093C>T	ENST00000405201.1	-	14	1497	c.1497G>A	c.(1495-1497)caG>caA	p.Q499Q	NCOR2_ENST00000397355.1_Silent_p.Q499Q|NCOR2_ENST00000404621.1_Silent_p.Q498Q|NCOR2_ENST00000404121.2_Silent_p.Q69Q|NCOR2_ENST00000429285.2_Silent_p.Q498Q|NCOR2_ENST00000356219.3_Silent_p.Q499Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	499	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.Q499Q(9)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gctgctgctgctgttgttgct	0.617																																					p.Q499Q													NCOR2_ENST00000405201,NS,carcinoma,0,11	NCOR2_ENST00000405201	0	11	9	Substitution - coding silent(9)	endometrium(4)|large_intestine(3)|kidney(2)	c.G1497A												9.0	10.0	10.0					12																	124887093		2051	4183	6234	SO:0001819	synonymous_variant	9612	exon16			CTGCTGCTGTTGT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1497G>A	12.37:g.124887093C>T			58	0	0		56	0.18	10	NM_006312	3	0.00	0	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																					0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000318173.2		NM_006312	
RP11-307N16.6	0	bcgsc.ca	37	13	24696846	24696846	+	Intron	SNP	G	G	A	rs17458394	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr13:24696846G>A	ENST00000382141.4	+	4	467				SPATA13_ENST00000424834.2_Intron																							ACATAATTACGAAGGAGGAGC	0.413													G|||	515	0.102835	0.0265	0.0778	5008	,	,		24031	0.12		0.1103	False		,,,				2504	0.1984				.													.	.			0			.																																									SO:0001627	intron_variant	100128337	.			AATTACGAAGGAG																												ENST00000382141.4:c.-111-100111G>A	13.37:g.24696846G>A			44	0	0		21	0.19	4	.	0		0		RNA	SNP	ENST00000382141.4	37																																																																																						0.413	RP11-307N16.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding		OTTHUMT00000472022.1			
TPTE2P6	374491	bcgsc.ca	37	13	24983385	24983385	+	IGR	SNP	G	G	T	rs1992390	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr13:24983385G>T								LINC00566 (72126 upstream) : PARP4 (11678 downstream)																							GGAAGTAAATGAGTGGATGGC	0.338													g|||	2211	0.441494	0.7262	0.3718	5008	,	,		19052	0.3204		0.4215	False		,,,				2504	0.2515				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTAAATGAGTGGA																													13.37:g.24983385G>T			605	0	0		453	0.05	23	.	0		0		RNA	SNP		37																																																																																					0	0.338										
UFM1	51569	hgsc.bcm.edu	37	13	38934869	38934869	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr13:38934869G>T	ENST00000239878.4	+	6	251	c.212G>T	c.(211-213)gGt>gTt	p.G71V	UFM1_ENST00000379641.1_Missense_Mutation_p.G89V|UFM1_ENST00000379649.1_Missense_Mutation_p.G89V	NM_016617.2	NP_057701.1	P61960	UFM1_HUMAN	ubiquitin-fold modifier 1	71					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				lung(2)|ovary(1)	3		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)		CTAAAACATGGTTCAGAACTG	0.269																																					p.G71V													.	.			0			c.G212T												105.0	99.0	101.0					13																	38934869		2202	4299	6501	SO:0001583	missense	51569	exon6			AACATGGTTCAGA	AF208844	CCDS9366.1, CCDS66533.1	13q13.3	2008-02-05	2005-05-27	2005-05-27	ENSG00000120686	ENSG00000120686			20597	protein-coding gene	gene with protein product		610553	"""chromosome 13 open reading frame 20"""	C13orf20		15071506	Standard	NM_001286706		Approved	bA131P10.1	uc001uwu.3	P61960	OTTHUMG00000017409	ENST00000239878.4:c.212G>T	13.37:g.38934869G>T	ENSP00000239878:p.Gly71Val		116	0	0		74	0.04	3	NM_016617	97	0.00	0	Q14346|Q5VXS0|Q6IAG6|Q9CPX2|Q9NZF2	Missense_Mutation	SNP	ENST00000239878.4	37	CCDS9366.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.149104	0.78001	.	.	ENSG00000120686	ENST00000379649;ENST00000239878;ENST00000379641	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.79215	0.4408	.	.	.	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	T	0.82376	-0.0488	8	0.87932	D	0	.	15.6788	0.77352	0.0:0.0:1.0:0.0	.	71	P61960	UFM1_HUMAN	V	89;71;89	.	ENSP00000239878:G71V	G	+	2	0	UFM1	37832869	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.131000	0.77243	2.312000	0.78011	0.650000	0.86243	GGT			0.269	UFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045989.1		NM_016617	
COX17P1	81993	bcgsc.ca	37	13	47065127	47065127	+	IGR	SNP	G	G	A	rs200135094	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr13:47065127G>A								RP11-189B4.6 (31807 upstream) : LRCH1 (62175 downstream)																							GGCCGCTGAAGCCCTGCTGCA	0.557													g|||	2	0.000399361	0.0	0.0	5008	,	,		16040	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	81993	.			GCTGAAGCCCTGC																													13.37:g.47065127G>A			362	0.0138121547	5		271	0.07	20	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.557										
DACH1	1602	broad.mit.edu	37	13	72440446	72440446	+	Silent	SNP	G	G	A			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr13:72440446G>A	ENST00000359684.2	-	1	461	c.462C>T	c.(460-462)agC>agT	p.S154S	DACH1_ENST00000354591.4_Silent_p.S154S|DACH1_ENST00000305425.4_Silent_p.S154S|DACH1_ENST00000313174.7_Silent_p.S154S			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	154	Poly-Ser.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		tgctactactgctgctgctgc	0.662																																					p.S154S													.	DACH1	123		0			c.C462T												3.0	4.0	4.0					13																	72440446		1701	3505	5206	SO:0001819	synonymous_variant	1602	exon1			ACTACTGCTGCTG	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"""dachshund homolog (Drosophila)"", ""dachshund homolog 1 (Drosophila)"""	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.462C>T	13.37:g.72440446G>A			21	0	0		27	0.11	3	NM_080759	0		0	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Silent	SNP	ENST00000359684.2	37																																																																																						0.662	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding		OTTHUMT00000045240.1		NM_004392	
Unknown	0	bcgsc.ca	37	14	22053729	22053729	+	IGR	SNP	G	G	A	rs17182620	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:22053729G>A								OR10G3 (14854 upstream) : TRAV1-1 (36261 downstream)																							CTTGTTGAGAGGATGTCTCAC	0.388													g|||	570	0.113818	0.0182	0.0951	5008	,	,		22769	0.2103		0.0626	False		,,,				2504	0.2096				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTGAGAGGATGTC																													14.37:g.22053729G>A			50	0.02	1		34	0.12	4	.	0		0		RNA	SNP		37																																																																																					0	0.388										
UBE2NP1	100288613	bcgsc.ca	37	14	22080350	22080350	+	IGR	SNP	G	G	T	rs7145928	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:22080350G>T								OR10G3 (41475 upstream) : TRAV1-1 (9640 downstream)																							CTGCCATTGCGTATTCTTCTG	0.393													G|||	1457	0.290935	0.2723	0.2305	5008	,	,		22519	0.4077		0.2445	False		,,,				2504	0.2863				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATTGCGTATTCT																													14.37:g.22080350G>T			152	0	0		115	0.06	7	.	0		0		RNA	SNP		37																																																																																					0	0.393										
UBE2NP1	100288613	bcgsc.ca	37	14	22080368	22080368	+	IGR	SNP	T	T	C	rs7152539	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:22080368T>C								OR10G3 (41493 upstream) : TRAV1-1 (9622 downstream)																							CTGGAAGGAATAGTTCAAGTT	0.408													T|||	1457	0.290935	0.2723	0.2305	5008	,	,		21813	0.4077		0.2445	False		,,,				2504	0.2863				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGGAATAGTTCA																													14.37:g.22080368T>C			151	0	0		111	0.05	6	.	0		0		RNA	SNP		37																																																																																					0	0.408										
TTC6	319089	bcgsc.ca;mdanderson.org	37	14	38266074	38266074	+	Silent	SNP	C	C	T	rs9805910	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:38266074C>T	ENST00000476979.1	+	4	431	c.144C>T	c.(142-144)gaC>gaT	p.D48D	TTC6_ENST00000382320.3_Silent_p.D31D|TTC6_ENST00000267368.7_Silent_p.D48D|TTC6_ENST00000553443.1_Silent_p.D1317D|TTC6_ENST00000554555.1_3'UTR			Q86TZ1	TTC6_HUMAN	tetratricopeptide repeat domain 6	48								p.D48D(1)		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)		AGGTCTTGGACGGAATCAGCT	0.428													C|||	1238	0.247204	0.0151	0.2795	5008	,	,		14880	0.2996		0.4264	False		,,,				2504	0.2996				.													TTC6,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.							C		418,3988	205.5+/-227.4	30,358,1815	107.0	98.0	101.0		2535	-10.1	0.0	14	dbSNP_119	101	3879,4721	543.3+/-384.4	849,2181,1270	no	coding-synonymous	TTC6	XM_002343299.3		879,2539,3085	TT,TC,CC		45.1047,9.4871,33.0386		845/971	38266074	4297,8709	2203	4300	6503	SO:0001819	synonymous_variant	319089	.			CTTGGACGGAATC	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.144C>T	14.37:g.38266074C>T			188	0	0		151	0.08	12	.	0		0	Q3SY88|Q96CE6	Silent	SNP	ENST00000476979.1	37																																																																																						0.428	TTC6-002	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000348621.2		XM_002343299	
MIA2	117153	broad.mit.edu	37	14	39716475	39716475	+	Frame_Shift_Del	DEL	C	C	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:39716475delC	ENST00000280082.3	+	4	896	c.697delC	c.(697-699)caafs	p.Q233fs	RP11-407N17.3_ENST00000553728.1_Frame_Shift_Del_p.Q233fs|MIA2_ENST00000556784.1_Frame_Shift_Del_p.Q232fs	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	233					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		GGGAGGAGAACAAGCTGAAGA	0.423																																					p.Q233fs													.	MIA2	82		0			c.697delC												83.0	83.0	83.0					14																	39716475		2203	4300	6503	SO:0001589	frameshift_variant	0	exon4			GGAGAACAAGCTG	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.697delC	14.37:g.39716475delC	ENSP00000280082:p.Gln233fs		214	0	0		209	0.03	7	NM_054024	0		0	A1L4H0|Q9H6C1	Frame_Shift_Del	DEL	ENST00000280082.3	37	CCDS9672.1																																																																																					0.423	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000276768.3		NM_054024	
DOCK11P1	100132537	bcgsc.ca	37	14	45329930	45329930	+	IGR	SNP	A	A	G	rs8016855	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45329930A>G								RP11-398E10.1 (77898 upstream) : RP11-857B24.1 (16146 downstream)																							TCATGTCCACATAAACAGAGG	0.388													G|||	1358	0.271166	0.7012	0.1354	5008	,	,		21155	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTCCACATAAACA																													14.37:g.45329930A>G			201	0	0		148	0.05	7	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45330315	45330315	+	IGR	SNP	A	A	G	rs17633092	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45330315A>G								RP11-398E10.1 (78283 upstream) : RP11-857B24.1 (15761 downstream)																							GACATTCGCCATACCAAATTT	0.353													A|||	298	0.0595048	0.0061	0.0331	5008	,	,		17282	0.1002		0.0497	False		,,,				2504	0.1186				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCGCCATACCAA																													14.37:g.45330315A>G			508	0.0039370079	2		449	0.04	16	.	0		0		RNA	SNP		37																																																																																					0	0.353										
DOCK11P1	100132537	bcgsc.ca	37	14	45330721	45330721	+	IGR	SNP	A	A	T	rs7149683	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45330721A>T								RP11-398E10.1 (78689 upstream) : RP11-857B24.1 (15355 downstream)																							TCCTTCTTCAACTATATTGGG	0.388													T|||	1301	0.259784	0.6604	0.1311	5008	,	,		18711	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTTCAACTATAT																													14.37:g.45330721A>T			161	0	0		143	0.06	9	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45331290	45331290	+	IGR	SNP	C	C	T	rs73345244	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45331290C>T								RP11-398E10.1 (79258 upstream) : RP11-857B24.1 (14786 downstream)																							TAAAACCTCACAGCAAAATGC	0.373													T|||	1301	0.259784	0.6604	0.1311	5008	,	,		21313	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACCTCACAGCAAA																													14.37:g.45331290C>T			195	0	0		194	0.09	17	.	0		0		RNA	SNP		37																																																																																					0	0.373										
DOCK11P1	100132537	bcgsc.ca	37	14	45331397	45331397	+	IGR	SNP	T	T	C	rs12323568	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45331397T>C								RP11-398E10.1 (79365 upstream) : RP11-857B24.1 (14679 downstream)																							ACACTTCAGATTGTCCATTTT	0.368													T|||	1355	0.270567	0.6997	0.134	5008	,	,		21690	0.1002		0.1093	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTCAGATTGTCCA																													14.37:g.45331397T>C			297	0.0033670034	1		301	0.06	17	.	0		0		RNA	SNP		37																																																																																					0	0.368										
DOCK11P1	100132537	bcgsc.ca	37	14	45331633	45331633	+	IGR	SNP	T	T	G	rs12323575	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45331633T>G								RP11-398E10.1 (79601 upstream) : RP11-857B24.1 (14443 downstream)																							CTACTAAGATTCTGAAGCCAG	0.413													G|||	1155	0.230631	0.559	0.1196	5008	,	,		19228	0.1002		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TAAGATTCTGAAG																													14.37:g.45331633T>G			373	0	0		309	0.10	30	.	0		0		RNA	SNP		37																																																																																					0	0.413										
DOCK11P1	100132537	bcgsc.ca	37	14	45332387	45332387	+	IGR	SNP	C	C	G	rs7161626	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45332387C>G								RP11-398E10.1 (80355 upstream) : RP11-857B24.1 (13689 downstream)																							CTCAGAAGTACACCAAACAAG	0.358													G|||	1157	0.23103	0.5605	0.1196	5008	,	,		21582	0.1002		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GAAGTACACCAAA																													14.37:g.45332387C>G			322	0	0		284	0.09	25	.	0		0		RNA	SNP		37																																																																																					0	0.358										
DOCK11P1	100132537	bcgsc.ca	37	14	45332752	45332752	+	IGR	SNP	G	G	A	rs74700367	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45332752G>A								RP11-398E10.1 (80720 upstream) : RP11-857B24.1 (13324 downstream)																							ATATGCCTTGGGAAATCTCTG	0.388													G|||	103	0.0205671	0.0265	0.0303	5008	,	,		20994	0.0		0.0408	False		,,,				2504	0.0061				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCCTTGGGAAATC																													14.37:g.45332752G>A			173	0.0115606936	2		132	0.06	8	.	0		0		RNA	SNP		37																																																																																					0	0.388										
DOCK11P1	100132537	bcgsc.ca	37	14	45333584	45333584	+	IGR	SNP	T	T	C	rs17115667	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45333584T>C								RP11-398E10.1 (81552 upstream) : RP11-857B24.1 (12492 downstream)																							TCAATTTTAATCTCATCATAG	0.338													T|||	1166	0.232827	0.5605	0.1196	5008	,	,		20786	0.1091		0.1054	False		,,,				2504	0.1288				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTTTAATCTCATC																													14.37:g.45333584T>C			233	0	0		172	0.05	8	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.338										
DOCK11P1	100132537	bcgsc.ca	37	14	45334503	45334503	+	IGR	SNP	C	C	A	rs8014660	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45334503C>A								RP11-398E10.1 (82471 upstream) : RP11-857B24.1 (11573 downstream)																							TTCTTTACATCAAATAAGGCA	0.418													C|||	1163	0.232228	0.562	0.1196	5008	,	,		18174	0.1091		0.1054	False		,,,				2504	0.1237				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTACATCAAATAA																													14.37:g.45334503C>A			194	0.0154639175	3		160	0.06	10	.	0		0		RNA	SNP		37																																																																																					0	0.418										
DOCK11P1	100132537	bcgsc.ca	37	14	45334686	45334686	+	IGR	SNP	C	C	T	rs17633300	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:45334686C>T								RP11-398E10.1 (82654 upstream) : RP11-857B24.1 (11390 downstream)																							AAAGTCCAACCTCTGAACTTC	0.363													C|||	304	0.0607029	0.0038	0.0331	5008	,	,		20088	0.1091		0.0497	False		,,,				2504	0.1186				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCCAACCTCTGAA																													14.37:g.45334686C>T			333	0.006006006	2		292	0.05	16	.	0		0		RNA	SNP		37																																																																																					0	0.363										
Unknown	0	bcgsc.ca	37	14	65066986	65066986	+	IGR	SNP	T	T	C	rs61987039	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:65066986T>C								RP11-973N13.3 (3732 upstream) : PLEKHG3 (104167 downstream)																							CAGTAAAATTTTGTGCAACTC	0.478													T|||	331	0.0660942	0.0061	0.0821	5008	,	,		18401	0.0		0.1362	False		,,,				2504	0.1319				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAAATTTTGTGCA																													14.37:g.65066986T>C			263	0.0038022814	1		233	0.04	10	.	9	0.00	0		RNA	SNP		37																																																																																					0	0.478										
CHORDC2P	317775	bcgsc.ca	37	14	90203530	90203530	+	RNA	SNP	G	G	C	rs72689476	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:90203530G>C	ENST00000555070.1	-	0	170																											ATGTGCTATTGCTTCTACTCG	0.373													G|||	1908	0.38099	0.1157	0.5634	5008	,	,		17442	0.3135		0.659	False		,,,				2504	0.3937				.													.	.			0			.																																											317775	.			GCTATTGCTTCTA																													14.37:g.90203530G>C			45	0	0		40	0.13	5	.	0		0		RNA	SNP	ENST00000555070.1	37																																																																																						0.373	RP11-33N16.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript		OTTHUMT00000411023.1			
AKT1	207	bcgsc.ca	37	14	105236681	105236681	+	Silent	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:105236681G>T	ENST00000554581.1	-	13	2920	c.1440C>A	c.(1438-1440)gcC>gcA	p.A480A	AKT1_ENST00000554192.1_Silent_p.A167A|AKT1_ENST00000554585.1_5'UTR|RP11-982M15.2_ENST00000557223.1_RNA|AKT1_ENST00000544168.1_Silent_p.A418A|AKT1_ENST00000402615.2_Silent_p.A480A|AKT1_ENST00000554848.1_Silent_p.A480A|AKT1_ENST00000407796.2_Silent_p.A480A|AKT1_ENST00000555528.1_Silent_p.A480A|AKT1_ENST00000555458.1_Intron|AKT1_ENST00000349310.3_Silent_p.A480A			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	480	AGC-kinase C-terminal.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CGCCGCCTCAGGCCGTGCCGC	0.592		1	Mis		"""breast, colorectal, ovarian, NSCLC"""																																p.A480A				Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379		0			c.C1440A												38.0	32.0	34.0					14																	105236681		2202	4299	6501	SO:0001819	synonymous_variant	207	exon14			GCCTCAGGCCGTG	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.1440C>A	14.37:g.105236681G>T			28	0	0		29	0.14	4	NM_005163	185	0.00	0	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																					0.592	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000410418.1		NM_005163	
AHNAK2	113146	broad.mit.edu	37	14	105418489	105418490	+	Frame_Shift_Ins	INS	-	-	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:105418489_105418490insG	ENST00000333244.5	-	7	3417_3418	c.3298_3299insC	c.(3298-3300)cagfs	p.Q1100fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1100						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GACGTCCACCTGGGGGCCCTTG	0.644																																					p.Q1100fs													.	AHNAK2	719		0			c.3299_3300insC																																									SO:0001589	frameshift_variant	113146	exon7			TCCACCTGGGGGC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3299dupC	14.37:g.105418494_105418494dupG	ENSP00000353114:p.Gln1100fs		181	0	0		175	0.03	5	NM_138420	0		0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Ins	INS	ENST00000333244.5	37	CCDS45177.1																																																																																					0.644	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000410300.1		NM_138420	
IGHA1	3493	bcgsc.ca	37	14	106174261	106174261	+	RNA	SNP	C	C	G	rs1407	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:106174261C>G	ENST00000390547.2	-	0	527							P01876	IGHA1_HUMAN	immunoglobulin heavy constant alpha 1						antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|protein-chromophore linkage (GO:0018298)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)										AGAGGTCACGCTCAGGTGGTC	0.617													.|||	1653	0.330072	0.146	0.513	5008	,	,		18227	0.3304		0.2833	False		,,,				2504	0.4969				.													.	.			0			.							C		753,3509		55,643,1433	32.0	40.0	37.0			2.5	0.0	14	dbSNP_36	37	2261,6211		247,1767,2222	no	intergenic				302,2410,3655	GG,GC,CC		26.6879,17.6678,23.6689			106174261	3014,9720	2131	4236	6367			3493	.			GTCACGCTCAGGT	J00220		14q32.33	2012-10-02			ENSG00000211895	ENSG00000211895		"""Immunoglobulins / IGH locus"""	5478	other	immunoglobulin gene		146900					Standard	NG_001019		Approved			P01876	OTTHUMG00000152494		14.37:g.106174261C>G			216	0	0		146	0.05	8	.	753	0.00	1		RNA	SNP	ENST00000390547.2	37																																																																																						0.617	IGHA1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene		OTTHUMT00000326459.1		NG_001019	
IGHV1-2	28474	bcgsc.ca;mdanderson.org	37	14	106452766	106452766	+	RNA	SNP	T	T	A	rs112806369	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:106452766T>A	ENST00000390594.2	-	0	319									immunoglobulin heavy variable 1-2																		ATGGTGACCCTGCCCTGAAAC	0.562													.|||	1608	0.321086	0.1831	0.3516	5008	,	,		8257	0.3095		0.4642	False		,,,				2504	0.3507				.													.	.			0			.							T		952,3150		113,726,1212	179.0	172.0	175.0			-2.1	0.3	14	dbSNP_132	175	3836,4538		916,2004,1267	no	intergenic				1029,2730,2479	AA,AT,TT		45.8085,23.2082,38.3777			106452766	4788,7688	2051	4187	6238			28474	.			TGACCCTGCCCTG	X07448		14q32.33	2012-02-08			ENSG00000211934	ENSG00000211934		"""Immunoglobulins / IGH locus"""	5550	other	immunoglobulin gene							Standard	NG_001019		Approved	V35			OTTHUMG00000152320		14.37:g.106452766T>A			618	0	0		518	0.05	24	.	563	0.01	3		RNA	SNP	ENST00000390594.2	37																																																																																						0.562	IGHV1-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325882.1		NG_001019	
IGHV3-38	28429	bcgsc.ca	37	14	106866588	106866588	+	RNA	SNP	T	T	C	rs73379082	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:106866588T>C	ENST00000390618.2	-	0	243									immunoglobulin heavy variable 3-38 (non-functional)																		GCCTGGCGGATCCAGCTCATC	0.587																																					.													.	.			0			.							T		1528,2796		2,1524,636	188.0	142.0	158.0			-4.8	0.3	14	dbSNP_130	158	837,7661		0,837,3412	no	intergenic				2,2361,4048	CC,CT,TT		9.8494,35.3377,18.4449			106866588	2365,10457	2162	4249	6411			28429	.			GGCGGATCCAGCT	M99669		14q32.33	2012-02-08	2008-08-22		ENSG00000211958	ENSG00000211958		"""Immunoglobulins / IGH locus"""	5601	other	immunoglobulin gene			"""immunoglobulin heavy variable 3-38"""				Standard	NG_001019		Approved				OTTHUMG00000152093		14.37:g.106866588T>C			163	0.0061349693	1		127	0.09	12	.	0		0		RNA	SNP	ENST00000390618.2	37																																																																																						0.587	IGHV3-38-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325190.1		NG_001019	
IGHV3-43	28426	bcgsc.ca;mdanderson.org	37	14	106926223	106926223	+	RNA	SNP	T	T	C	rs530460516|rs2467912	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:106926223T>C	ENST00000434710.1	-	0	398									immunoglobulin heavy variable 3-43																		GTGTCCTCAGTTCTCAGACTG	0.507																																					.													.	.			0			.							C		1642,2420		18,1606,407	294.0	210.0	237.0			-3.8	0.0	14	dbSNP_100	237	2211,6153		150,1911,2121	no	intergenic				168,3517,2528	CC,CT,TT		26.4347,40.4234,31.0076			106926223	3853,8573	2031	4182	6213			28426	.			CCTCAGTTCTCAG	M99672		14q32.33	2012-02-08			ENSG00000232216	ENSG00000232216		"""Immunoglobulins / IGH locus"""	5604	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152094		14.37:g.106926223T>C			205	0.0048780488	1		182	0.07	12	.	57	0.00	0		RNA	SNP	ENST00000434710.1	37																																																																																						0.507	IGHV3-43-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325191.1		NG_001019	
IGHV3-43	28426	bcgsc.ca;mdanderson.org	37	14	106926287	106926287	+	RNA	SNP	G	G	A	rs2467911|rs566955550	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:106926287G>A	ENST00000434710.1	-	0	334									immunoglobulin heavy variable 3-43																		TGGTGAATCGGCCCTTCACAG	0.498																																					.													.	.			0			.							G		1649,2383		20,1609,387	267.0	188.0	214.0			2.0	0.3	14	dbSNP_100	214	2221,6083		151,1919,2082	no	intergenic				171,3528,2469	AA,AG,GG		26.7461,40.8978,31.3716			106926287	3870,8466	2016	4152	6168			28426	.			GAATCGGCCCTTC	M99672		14q32.33	2012-02-08			ENSG00000232216	ENSG00000232216		"""Immunoglobulins / IGH locus"""	5604	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152094		14.37:g.106926287G>A			156	0	0		143	0.10	14	.	66	0.00	0		RNA	SNP	ENST00000434710.1	37																																																																																						0.498	IGHV3-43-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000325191.1		NG_001019	
IGHV1-69	28461	bcgsc.ca;mdanderson.org	37	14	107170005	107170005	+	RNA	SNP	T	T	C	rs1141720	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:107170005T>C	ENST00000390633.2	-	0	337									immunoglobulin heavy variable 1-69																		CTCGTGGATTTGTCCGCGGTA	0.542													.|||	2488	0.496805	0.6188	0.5274	5008	,	,		24628	0.4891		0.501	False		,,,				2504	0.3139				.													.	.			0			.							C		2577,1623		564,1449,87	315.0	259.0	277.0			-0.5	0.0	14	dbSNP_86	277	4128,4274		547,3034,620	no	intergenic				1111,4483,707	CC,CT,TT		49.1312,38.6429,46.7942			107170005	6705,5897	2100	4201	6301			28461	.			TGGATTTGTCCGC	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.107170005T>C			105	0.0095238095	1		105	0.07	7	.	200	0.01	1		RNA	SNP	ENST00000390633.2	37																																																																																						0.542	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	107178938	107178938	+	RNA	SNP	T	T	C	rs17113976	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr14:107178938T>C	ENST00000390634.2	-	0	314									immunoglobulin heavy variable 2-70																		AGATGTGCTGTAGTATTTATC	0.527													.|||	657	0.13119	0.326	0.062	5008	,	,		12416	0.0962		0.0328	False		,,,				2504	0.0542				.													.	.			0			.							T		959,3165		0,959,1103	194.0	147.0	163.0			-1.5	0.0	14	dbSNP_123	163	181,8173		0,181,3996	no	intergenic				0,1140,5099	CC,CT,TT		2.1666,23.2541,9.1361			107178938	1140,11338	2062	4177	6239			28454	.			GTGCTGTAGTATT	L21969		14q32.33	2012-02-08			ENSG00000211974	ENSG00000211974		"""Immunoglobulins / IGH locus"""	5577	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151870		14.37:g.107178938T>C			344	0	0		263	0.03	7	.	19	0.00	0		RNA	SNP	ENST00000390634.2	37																																																																																						0.527	IGHV2-70-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000324215.1		NG_001019	
HERC2P10	390561	bcgsc.ca	37	15	31129037	31129037	+	IGR	SNP	G	G	A	rs11070624	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr15:31129037G>A								AC004460.1 (35446 upstream) : FAN1 (67017 downstream)																							GCCTGGTTCCGGAGGTACTGC	0.527													g|||	2648	0.528754	0.2118	0.5173	5008	,	,		21115	0.8264		0.496	False		,,,				2504	0.6922				.													.	.			0			.																																									SO:0001628	intergenic_variant	390561	.			GGTTCCGGAGGTA																													15.37:g.31129037G>A			352	0.0198863636	7		339	0.06	19	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.527										
AGBL1	123624	broad.mit.edu	37	15	87066164	87066165	+	Frame_Shift_Ins	INS	-	-	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr15:87066164_87066165insC	ENST00000441037.2	+	18	2636_2637	c.2541_2542insC	c.(2542-2544)cccfs	p.P848fs	AGBL1_ENST00000389298.3_Frame_Shift_Ins_p.P579fs|AGBL1_ENST00000421325.2_Frame_Shift_Ins_p.P848fs	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	848					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TTGGCCGAAGTCCCGTGGTGAG	0.51																																					p.S847fs													.	AGBL1	151		0			c.2541_2542insC																																									SO:0001589	frameshift_variant	123624	exon18			CCGAAGTCCCGTG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2544dupC	15.37:g.87066167_87066167dupC	ENSP00000413001:p.Pro848fs		257	0	0		243	0.02	6	NM_152336	0		0	A1A4X5|A6NJH6|C9JHL5	Frame_Shift_Ins	INS	ENST00000441037.2	37	CCDS58398.1																																																																																					0.510	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000314929.5		NM_152336	
RP11-266O8.1	0	bcgsc.ca	37	15	93974276	93974276	+	lincRNA	SNP	C	C	G	rs28539148	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr15:93974276C>G	ENST00000543286.1	+	0	545																											TAACGGCTCCCAGAAACTGCT	0.478													C|||	710	0.141773	0.1127	0.1081	5008	,	,		17095	0.2143		0.1561	False		,,,				2504	0.1155				.													.	.			0			.																																											0	.			GGCTCCCAGAAAC																													15.37:g.93974276C>G			117	0	0		137	0.07	10	.	0		0		RNA	SNP	ENST00000543286.1	37																																																																																						0.478	RP11-266O8.1-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000415156.1			
DNM1P47	100216544	broad.mit.edu	37	15	102312710	102312710	+	RNA	SNP	A	A	G	rs116458034	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr15:102312710A>G	ENST00000561463.1	+	0	14078				RN7SL209P_ENST00000488309.2_RNA					DNM1 pseudogene 47																		ATGGGTTCACATCTCGGCAGT	0.572													.|||	157	0.0313498	0.0794	0.0259	5008	,	,		19011	0.0		0.0249	False		,,,				2504	0.0092				.													.	.			0			.																																											0	.			GTTCACATCTCGG	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102312710A>G			27	0	0		23	0.13	3	.	3	0.00	0		RNA	SNP	ENST00000561463.1	37																																																																																						0.572	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000417589.1		NG_009149	
C16orf90	646174	broad.mit.edu	37	16	3546140	3546141	+	5'Flank	INS	-	-	A	rs200618809|rs74546027		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr16:3546140_3546141insA	ENST00000437192.3	-	0	0				LA16c-306E5.3_ENST00000574423.2_RNA	NM_001080524.1	NP_001073993.1	A8MZG2	CP090_HUMAN	chromosome 16 open reading frame 90											large_intestine(1)	1						gactccgtctcaaaaaaaaaaa	0.559																																					.													.	C16orf90	16		0			.																																									SO:0001631	upstream_gene_variant	0	.			CCGTCTCAAAAAA		CCDS45397.1	16p13.3	2009-01-29			ENSG00000215131	ENSG00000215131			34455	protein-coding gene	gene with protein product							Standard	NM_001080524		Approved	LOC646174	uc002cvi.3	A8MZG2	OTTHUMG00000154627		16.37:g.3546151_3546151dupA	Exception_encountered		5	0	0		5	0.40	2	.	0		0		RNA	INS	ENST00000437192.3	37	CCDS45397.1																																																																																					0.559	C16orf90-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000346319.2		NM_001080524	
CNGB1	1258	ucsc.edu;mdanderson.org	37	16	57937856	57937856	+	Silent	SNP	C	C	T	rs413562	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr16:57937856C>T	ENST00000251102.8	-	27	2724	c.2664G>A	c.(2662-2664)gcG>gcA	p.A888A	CNGB1_ENST00000564448.1_Silent_p.A882A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	888					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AGGTCTGTCCGGCGGTGGCGG	0.572																																					p.A888A	Colon(156;1293 1853 16336 28962 38659)												.	CNGB1	105		0			c.C2664A												82.0	84.0	83.0					16																	57937856		2033	4175	6208	SO:0001819	synonymous_variant	1258	exon27			CTGTCCGGCGGTG	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2664G>A	16.37:g.57937856C>T			74	0	0		81	0.11	9	NM_001297	0		0	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																					0.572	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000337167.2		NM_001297	
HYDIN	54768	bcgsc.ca	37	16	71101279	71101279	+	Silent	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr16:71101279G>T	ENST00000393567.2	-	15	2139	c.1989C>A	c.(1987-1989)tcC>tcA	p.S663S	HYDIN_ENST00000541601.1_Silent_p.S680S|HYDIN_ENST00000288168.10_Silent_p.S680S|HYDIN_ENST00000448691.1_Silent_p.S663S|HYDIN_ENST00000321489.5_Silent_p.S663S|HYDIN_ENST00000448089.2_Silent_p.S663S|HYDIN_ENST00000393550.2_Silent_p.S678S|HYDIN_ENST00000538248.1_Silent_p.S690S|HYDIN_ENST00000543639.1_5'Flank	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	663					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCACAGTGTTGGAGCATAATG	0.537																																					p.S690S													.	HYDIN	788		0			c.C2070A												74.0	62.0	66.0					16																	71101279		2198	4299	6497	SO:0001819	synonymous_variant	54768	exon15			AGTGTTGGAGCAT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1989C>A	16.37:g.71101279G>T			59	0.0169491525	1		50	0.08	4	NM_001198542	3	0.00	0	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.275216	0.23307	.	.	ENSG00000157423	ENST00000542890	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	T	0.73377	0.3579	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73007	-0.4118	4	.	.	.	.	17.1332	0.86732	0.0:0.0:1.0:0.0	.	.	.	.	Q	65	.	.	P	-	2	0	HYDIN	69658780	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.872000	0.56085	2.332000	0.79248	0.603000	0.83216	CCA			0.537	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000398624.3			
PKD1L2	114780	broad.mit.edu	37	16	81155069	81155069	+	RNA	DEL	A	A	-	rs557576474		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr16:81155069delA	ENST00000534142.1	-	0	1000				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000533478.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						actccatctcaaaaaaaaaaa	0.527																																					.													.	PKD1L2	361		0			.																																											114780	.			CATCTCAAAAAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81155069delA			7	0	0		6	0.50	3	.	1	0.00	0	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	RNA	DEL	ENST00000534142.1	37																																																																																						0.527	PKD1L2-009	PUTATIVE	basic|exp_conf	processed_transcript	polymorphic_pseudogene		OTTHUMT00000387969.1			
VMO1	284013	bcgsc.ca	37	17	4689195	4689195	+	Intron	DEL	C	C	-	rs3215170|rs398030211	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:4689195delC	ENST00000328739.5	-	2	391				VMO1_ENST00000441199.2_Splice_Site|VMO1_ENST00000354194.4_Intron|VMO1_ENST00000416307.2_Intron	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)							extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						AAGGGACATACCATCACCCCA	0.627													CC|CC|C|deletion	2132	0.425719	0.2504	0.3876	5008	,	,		18851	0.4514		0.4284	False		,,,				2504	0.6605				.													.	VMO1	19		0			c.347+1G>-								,,,	1262,3002		170,922,1040	171.0	133.0	146.0		,,,	-1.5	0.0	17	dbSNP_106	222	3482,4772		742,1998,1387	no	intron,intron,intron,splice-5	VMO1	NM_182566.2,NM_001144941.1,NM_001144940.1,NM_001144939.1	,,,	912,2920,2427	A1A1,A1R,RR		42.1856,29.5966,37.8974	,,,	,,,	4689195	4744,7774	2194	4226	6420	SO:0001627	intron_variant	284013	exon3			GACATACCATCAC	AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.311+36G>-	17.37:g.4689195delC			96	0	0		95	0.11	10	NM_001144939	0		0	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Splice_Site	DEL	ENST00000328739.5	37	CCDS11055.1																																																																																					0.627	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000439587.1		NM_182566	
Unknown	0	bcgsc.ca	37	17	16796691	16796691	+	IGR	SNP	C	C	T	rs6502530	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:16796691C>T								AC022596.2 (43019 upstream) : TBC1D27 (29537 downstream)																							CCAACCTCCACGGCAGGTGCA	0.498													C|||	2071	0.413538	0.3722	0.5447	5008	,	,		19177	0.2619		0.5119	False		,,,				2504	0.4315				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTCCACGGCAGG																													17.37:g.16796691C>T			88	0	0		69	0.12	8	.	0		0		RNA	SNP		37																																																																																					0	0.498										
AC007952.5	0	broad.mit.edu	37	17	18996545	18996545	+	Frame_Shift_Del	DEL	G	G	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:18996545delG	ENST00000428928.1	+	1	259	c.41delG	c.(40-42)tgcfs	p.C14fs	AC007952.5_ENST00000443876.1_Frame_Shift_Del_p.C14fs|RP11-160E2.19_ENST00000583141.1_lincRNA|AC007952.5_ENST00000399093.1_5'UTR|AC007952.5_ENST00000399091.1_5'UTR																							tttgagacctgcttgttcatg	0.567																																					.													.	.			0			.																																									SO:0001589	frameshift_variant	0	.			AGACCTGCTTGTT																												ENST00000428928.1:c.41delG	17.37:g.18996545delG	ENSP00000395460:p.Cys14fs		1048	0	0		927	0.01	10	.	0		0		Frame_Shift_Del	DEL	ENST00000428928.1	37																																																																																						0.567	AC007952.5-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding					
LOC100287072	100287072	bcgsc.ca	37	17	20619842	20619842	+	RNA	SNP	A	A	G	rs112468000	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:20619842A>G	ENST00000578210.1	+	0	49					NR_073509.1																						ACAAAAGCAGAATGGAATATT	0.343													a|||	104	0.0207668	0.0008	0.0202	5008	,	,		18396	0.0		0.0427	False		,,,				2504	0.047				.													.	.			0			.																																											0	.			AAGCAGAATGGAA																													17.37:g.20619842A>G			280	0	0		245	0.03	8	.	5	0.00	0		RNA	SNP	ENST00000578210.1	37																																																																																						0.343	AC126365.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000443937.1			
RP11-344E13.3	0	bcgsc.ca	37	17	20805348	20805348	+	RNA	SNP	A	A	G	rs57960567	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:20805348A>G	ENST00000577537.1	+	0	714				RP11-344E13.3_ENST00000417232.2_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RP11-344E13.3_ENST00000582324.1_RNA|RP11-344E13.3_ENST00000577860.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA																							CTCTTTGTTGATCACCTCTTT	0.453													a|||	1258	0.251198	0.1694	0.2839	5008	,	,		19095	0.3313		0.2247	False		,,,				2504	0.2832				.													.	.			0			.																																											284203	.			TTGTTGATCACCT																													17.37:g.20805348A>G			190	0	0		206	0.05	10	.	5	0.00	0		RNA	SNP	ENST00000577537.1	37																																																																																						0.453	RP11-344E13.3-001	KNOWN	basic	antisense	antisense		OTTHUMT00000444041.1			
TUFMP1	645668	bcgsc.ca	37	17	25409812	25409812	+	IGR	SNP	G	G	A	rs2061899	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:25409812G>A								RP11-260A9.6 (82861 upstream) : RP11-663N22.1 (155072 downstream)																							TCAGGGTGAAGCACTGGCCTT	0.532													a|||	2355	0.470248	0.6369	0.451	5008	,	,		19936	0.506		0.328	False		,,,				2504	0.3681				.													.	.			0			.																																									SO:0001628	intergenic_variant	645668	.			GGTGAAGCACTGG																													17.37:g.25409812G>A			98	0.0102040816	1		123	0.05	6	.	0		0		RNA	SNP		37																																																																																					0	0.532										
NOS2P1	645740	bcgsc.ca	37	17	25982851	25982851	+	IGR	SNP	A	A	T	rs9897292	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:25982851A>T								LGALS9 (6265 upstream) : RP11-19P22.5 (5723 downstream)																							AGGGGTGCTTACTTCCGCACA	0.637													A|||	1565	0.3125	0.3139	0.3775	5008	,	,		17580	0.2946		0.2674	False		,,,				2504	0.3292				.													.	.			0			.																																									SO:0001628	intergenic_variant	645740	.			GTGCTTACTTCCG																													17.37:g.25982851A>T			54	0	0		78	0.12	9	.	0		0		Splice_Site	SNP		37																																																																																					0	0.637										
KRT32	3882	bcgsc.ca	37	17	39619093	39619094	+	Missense_Mutation	DNP	GT	GT	AC	rs2604954|rs2604955|rs386797091|rs70964671	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GT	GT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:39619093_39619094GT>AC	ENST00000225899.3	-	6	1308_1309	c.1205_1206AC>GT	c.(1204-1206)aAC>aGT	p.N402S		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	402	Coil 2.|Rod.		N -> S (in dbSNP:rs2604955). {ECO:0000269|PubMed:7556444, ECO:0000269|PubMed:8823373}.		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				TGCAGTCCTCGTTCTCCAGCAG	0.619																																					p.N402S													.	KRT32	57		0			c.A1205G																																									SO:0001583	missense	3882	exon6			GTCCTCGTTCTCC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1205_1206delinsAC	17.37:g.39619093_39619094delinsAC	ENSP00000225899:p.Asn402Ser		160	0	0		115	0.09	10	NM_002278	6	0.00	0		Missense_Mutation	DNP	ENST00000225899.3	37	CCDS11393.1																																																																																					0.619	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257293.1		NM_002278	
DND1P1	644157	bcgsc.ca	37	17	43663247	43663247	+	IGR	SNP	C	C	A	rs1724390	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:43663247C>A								RP11-798G7.6 (22651 upstream) : CRHR1-IT1 (34728 downstream)																							ATGCAGTCCACGCGGGATTGT	0.562													N|||	443	0.0884585	0.0159	0.1614	5008	,	,		17419	0.001		0.2435	False		,,,				2504	0.0654				.													.	.			0			.																																									SO:0001628	intergenic_variant	644157	.			AGTCCACGCGGGA																													17.37:g.43663247C>A			32	0	0		35	0.34	12	.	0		0		RNA	SNP		37																																																																																					0	0.562										
Unknown	0	bcgsc.ca	37	17	44336943	44336943	+	IGR	SNP	C	C	T	rs573489348		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:44336943C>T								KANSL1 (35769 upstream) : RP11-259G18.1 (7459 downstream)																							CCTGCCTCAGCCCCAGCAGAC	0.597																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTCAGCCCCAGC																													17.37:g.44336943C>T			221	0	0		216	0.08	18	.	58	0.00	0		RNA	SNP		37																																																																																					0	0.597										
Unknown	0	bcgsc.ca	37	17	44337209	44337209	+	IGR	SNP	C	C	T	rs112008792		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:44337209C>T								KANSL1 (36035 upstream) : RP11-259G18.1 (7193 downstream)																							CAGGGTAGCCCGAGCCCCTTG	0.627																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTAGCCCGAGCCC																													17.37:g.44337209C>T			156	0	0		205	0.04	9	.	33	0.00	0		RNA	SNP		37																																																																																					0	0.627										
RP11-259G18.1	0	bcgsc.ca	37	17	44344738	44344749	+	RNA	DEL	GCTGGTGACCCT	GCTGGTGACCCT	-	rs67539917|rs200890045	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GCTGGTGACCCT	GCTGGTGACCCT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:44344738_44344749delGCTGGTGACCCT	ENST00000570002.2	+	0	336_347																											CGGGCATCTGGCTGGTGACCCTGCTGGTGGAT	0.59														368	0.0734824	0.0113	0.1412	5008	,	,		20359	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			CATCTGGCTGGTG																													17.37:g.44344738_44344749delGCTGGTGACCCT			92	0	0		90	0.03	3	.	5	0.00	0		RNA	DEL	ENST00000570002.2	37																																																																																						0.590	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-259G18.1	0	bcgsc.ca	37	17	44344822	44344822	+	RNA	SNP	G	G	A	rs76934998	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:44344822G>A	ENST00000570002.2	+	0	420																											TTCTTCTTCCGAGTCCACATG	0.542													.|||	368	0.0734824	0.0113	0.1412	5008	,	,		22066	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			TCTTCCGAGTCCA																													17.37:g.44344822G>A			151	0.0066225166	1		128	0.10	13	.	10	0.00	0		RNA	SNP	ENST00000570002.2	37																																																																																						0.542	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
RP11-259G18.1	0	bcgsc.ca	37	17	44344858	44344858	+	RNA	SNP	A	A	G	rs74358353	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:44344858A>G	ENST00000570002.2	+	0	456																											TCCAGCTGCAATAAACCGTGT	0.517													.|||	368	0.0734824	0.0113	0.1412	5008	,	,		24369	0.001		0.2008	False		,,,				2504	0.0532				.													.	.			0			.																																											0	.			GCTGCAATAAACC																													17.37:g.44344858A>G			138	0	0		111	0.12	13	.	4	0.00	0		RNA	SNP	ENST00000570002.2	37																																																																																						0.517	RP11-259G18.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000431423.2			
LOC101927755	101927755	broad.mit.edu	37	17	58054437	58054438	+	lincRNA	INS	-	-	A	rs568051664	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:58054437_58054438insA	ENST00000586209.1	+	0	158																											catgcttacagaaaaaaaaatg	0.287													aaaaaaaaaa|AAAAAAAAA|AAAAAAAAAA|deletion	12	0.00239617	0.0083	0.0014	5008	,	,		16538	0.0		0.0	False		,,,				2504	0.0				.													.	.			0			.																																											0	.			CTTACAGAAAAAA																													17.37:g.58054446_58054446dupA			10	0	0		12	0.17	2	.	0		0		RNA	INS	ENST00000586209.1	37																																																																																						0.287	RP11-178C3.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000449162.1			
POLRMTP1	284167	bcgsc.ca	37	17	60214389	60214389	+	IGR	SNP	G	G	A	rs72844475	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr17:60214389G>A								Y_RNA (14607 upstream) : TBC1D3P2 (127676 downstream)																							CCTGGCTTGGGCACCGCCTGC	0.572													G|||	1531	0.305711	0.289	0.5144	5008	,	,		16916	0.1359		0.3986	False		,,,				2504	0.2597				.													.	.			0			.																																									SO:0001628	intergenic_variant	284167	.			GCTTGGGCACCGC																													17.37:g.60214389G>A			51	0	0		65	0.08	5	.	70	0.00	0		RNA	SNP		37																																																																																					0	0.572										
ZNF44	51710	hgsc.bcm.edu;broad.mit.edu	37	19	12384353	12384353	+	Frame_Shift_Del	DEL	G	G	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:12384353delG	ENST00000356109.5	-	5	979	c.861delC	c.(859-861)tccfs	p.S287fs	ZNF44_ENST00000355684.5_Frame_Shift_Del_p.S239fs	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		GTCTTAGATAGGAACTGTAAA	0.378																																					p.Y288fs													.	ZNF44	55		0			c.862delT												115.0	123.0	120.0					19																	12384353		2202	4297	6499	SO:0001589	frameshift_variant	51710	exon5			TAGATAGGAACTG	X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.861delC	19.37:g.12384353delG	ENSP00000348419:p.Ser287fs		162	0	0		157	0.07	11	NM_001164276	36	0.00	0	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Frame_Shift_Del	DEL	ENST00000356109.5	37	CCDS54223.1																																																																																					0.378	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000344132.1		NM_016264	
ZNF799	90576	broad.mit.edu	37	19	12501744	12501745	+	Frame_Shift_Ins	INS	-	-	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:12501744_12501745insT	ENST00000430385.3	-	4	1667_1668	c.1467_1468insA	c.(1465-1470)caatacfs	p.Y490fs	ZNF799_ENST00000419318.1_Frame_Shift_Ins_p.Y458fs|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TGAGAAAGGTATTGGAAACAAC	0.366																																					p.Y490fs													.	ZNF799	111		0			c.1468_1469insA																																									SO:0001589	frameshift_variant	90576	exon4			AAAGGTATTGGAA	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1468dupA	19.37:g.12501746_12501746dupT	ENSP00000411084:p.Tyr490fs		215	0	0		226	0.03	7	NM_001080821	16	0.00	0		Frame_Shift_Ins	INS	ENST00000430385.3	37	CCDS45989.1																																																																																					0.366	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000344099.2		NM_001080821	
CYP4F9P	100506916	bcgsc.ca	37	19	16091763	16091763	+	IGR	SNP	T	T	C	rs8103740	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:16091763T>C								OR10H4 (30995 upstream) : LINC00661 (34680 downstream)																							GTGATCTCTCTTTGCTATTCT	0.562													C|||	279	0.0557109	0.1399	0.036	5008	,	,		18019	0.001		0.0378	False		,,,				2504	0.0307				.													.	.			0			.																																									SO:0001628	intergenic_variant	100506916	.			TCTCTCTTTGCTA																													19.37:g.16091763T>C			43	0	0		48	0.10	5	.	0		0		RNA	SNP		37																																																																																					0	0.562										
GPI	2821	bcgsc.ca	37	19	34856274	34856274	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:34856274G>T	ENST00000356487.5	+	1	344	c.103G>T	c.(103-105)Gac>Tac	p.D35Y	GPI_ENST00000586425.1_Missense_Mutation_p.D35Y|GPI_ENST00000415930.3_Missense_Mutation_p.D74Y	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	35					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					TGCCAACAAGGACCGCTTCAA	0.731																																					p.D74Y													.	GPI	63		0			c.G220T												23.0	25.0	24.0					19																	34856274		2201	4297	6498	SO:0001583	missense	2821	exon2			AACAAGGACCGCT	M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"""glucose phosphate isomerase"""			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.103G>T	19.37:g.34856274G>T	ENSP00000348877:p.Asp35Tyr		32	0	0		21	0.19	4	NM_001184722	224	0.00	0	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Missense_Mutation	SNP	ENST00000356487.5	37	CCDS12437.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.74|16.74	3.208201|3.208201	0.58343|0.58343	.|.	.|.	ENSG00000105220|ENSG00000105220	ENST00000415930;ENST00000356487|ENST00000392234	D;D|.	0.94046|.	-3.34;-3.34|.	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	0.421961|.	0.29466|.	N|.	0.012068|.	T|T	0.75657|0.75657	0.3879|0.3879	L|L	0.53561|0.53561	1.675|1.675	0.46499|0.46499	D|D	0.999077|0.999077	B;P;B;B|D	0.47409|0.89917	0.068;0.895;0.068;0.088|1.0	B;P;B;B|D	0.46758|0.74023	0.078;0.526;0.078;0.052|0.982	T|T	0.78272|0.78272	-0.2268|-0.2268	10|8	0.87932|0.87932	D|D	0|0	-20.1644|-20.1644	17.736|17.736	0.88392|0.88392	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	35;74;35;35|37	B4DE36;B4DG39;B4DVJ0;P06744|Q59F85	.;.;.;G6PI_HUMAN|.	Y|V	74;35|37	ENSP00000405573:D74Y;ENSP00000348877:D35Y|.	ENSP00000348877:D35Y|ENSP00000376067:G37V	D|G	+|+	1|2	0|0	GPI|GPI	39548114|39548114	1.000000|1.000000	0.71417|0.71417	0.217000|0.217000	0.23759|0.23759	0.004000|0.004000	0.04260|0.04260	6.126000|6.126000	0.71635|0.71635	2.528000|2.528000	0.85240|0.85240	0.462000|0.462000	0.41574|0.41574	GAC|GGA			0.731	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000451693.3			
CTBP2P7	401914	bcgsc.ca	37	19	36989005	36989005	+	IGR	SNP	C	C	T	rs2945970	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:36989005C>T								CTD-2630F21.1 (7063 upstream) : ZNF260 (12591 downstream)																							AGCCATCCAGCGGCGCCAGCA	0.592													C|||	2300	0.459265	0.5234	0.3804	5008	,	,		18889	0.255		0.5507	False		,,,				2504	0.545				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATCCAGCGGCGCC																													19.37:g.36989005C>T			51	0	0		61	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.592										
SUPT5H	6829	hgsc.bcm.edu	37	19	39944127	39944128	+	Frame_Shift_Ins	INS	-	-	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:39944127_39944128insC	ENST00000599117.1	+	4	574_575	c.207_208insC	c.(208-210)cccfs	p.P70fs	SUPT5H_ENST00000359191.6_Frame_Shift_Ins_p.P70fs|SUPT5H_ENST00000402194.2_Frame_Shift_Ins_p.P70fs|SUPT5H_ENST00000432763.2_Frame_Shift_Ins_p.P70fs|SUPT5H_ENST00000598725.1_Frame_Shift_Ins_p.P70fs			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	70	Glu-rich.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CCCCCAAGAAACCCCGCCATGG	0.515																																					p.K69fs													.	SUPT5H	119		0			c.207_208insC																																									SO:0001589	frameshift_variant	6829	exon3			CAAGAAACCCCGC	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.211dupC	19.37:g.39944131_39944131dupC	ENSP00000470252:p.Pro70fs		113	0	0		145	0.06	9	NM_001130825	163	0.00	0	O43279|Q59G52|Q99639	Frame_Shift_Ins	INS	ENST00000599117.1	37	CCDS12536.1																																																																																					0.515	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000464918.1		NM_003169	
CYP2F2P	171427	bcgsc.ca	37	19	41332171	41332171	+	Intron	SNP	C	C	T	rs78011401	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:41332171C>T	ENST00000601627.1	+	1	119																											GGGAAGATGTCGTACAACTGG	0.592													.|||	1386	0.276757	0.0242	0.4164	5008	,	,		13641	0.3502		0.3211	False		,,,				2504	0.3978				.													.	.			0			.																																									SO:0001627	intron_variant	171427	.			AGATGTCGTACAA																												ENST00000601627.1:c.119+24851C>T	19.37:g.41332171C>T			253	0	0		231	0.05	11	.	11	0.00	0		RNA	SNP	ENST00000601627.1	37																																																																																						0.592	CTC-490E21.12-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding		OTTHUMT00000463921.1			
CYP2A7P1	1550	ucsc.edu	37	19	41531656	41531656	+	IGR	SNP	A	A	C	rs7249735	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:41531656A>C								CYP2B6 (7353 upstream) : CYP2A13 (62720 downstream)																							AAGGTGGGATAGATGCTGGAG	0.532													C|||	1669	0.333267	0.4107	0.4553	5008	,	,		16860	0.1677		0.2773	False		,,,				2504	0.3701				.													.	.			0			.																																									SO:0001628	intergenic_variant	1550	.			TGGGATAGATGCT																													19.37:g.41531656A>C			41	0	0		41	0.10	4	.	0		0		Missense_Mutation	SNP		37		631	0.2889194139194139	191	0.3882113821138211	157	0.43370165745856354	84	0.14685314685314685	199	0.262532981530343	N	0.001	-3.100413	0.00033	.	.	ENSG00000213908	ENST00000301171	.	.	.	3.21	2.14	0.27477	.	0.238965	0.39407	N	0.001379	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44787	-0.9305	5	0.02654	T	1	.	7.1172	0.25423	0.1967:0.6132:0.1901:0.0	rs7249735;rs52822731;rs7249735	.	.	.	D	163	.	ENSP00000301171:Y163D	Y	-	1	0	CYP2A7P1	46223496	0.259000	0.24043	0.186000	0.23195	0.003000	0.03518	0.533000	0.23082	0.053000	0.16036	-3.327000	0.00044	TAT		0	0.532										
HIF3A	64344	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	46828803	46828803	+	Silent	SNP	A	A	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:46828803A>G	ENST00000377670.4	+	11	1378	c.1347A>G	c.(1345-1347)ccA>ccG	p.P449P	HIF3A_ENST00000472815.1_Silent_p.P380P|HIF3A_ENST00000420102.2_Silent_p.P398P|HIF3A_ENST00000339613.2_Silent_p.P393P|HIF3A_ENST00000600383.1_Silent_p.P380P|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000300862.3_Silent_p.P447P|HIF3A_ENST00000244303.6_Silent_p.P380P	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	449					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CTGATCTCCCAGATGAACTAC	0.498																																					p.P449P													HIF3A_ENST00000377670,NS,carcinoma,0,2	HIF3A_ENST00000377670	0	2	0			c.A1347G												152.0	152.0	152.0					19																	46828803		2203	4300	6503	SO:0001819	synonymous_variant	64344	exon11			TCTCCCAGATGAA	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1347A>G	19.37:g.46828803A>G			70	0.0142857143	1		62	0.21	13	NM_152795	4	0.00	0	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Silent	SNP	ENST00000377670.4	37	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	A	10.25	1.297978	0.23650	.	.	ENSG00000124440	ENST00000472815	.	.	.	4.57	-0.949	0.10376	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37820	-0.9689	4	.	.	.	.	4.9752	0.14136	0.3745:0.2038:0.4216:0.0	.	.	.	.	G	422	.	.	R	+	1	2	HIF3A	51520643	0.616000	0.27035	0.735000	0.30896	0.968000	0.65278	-0.233000	0.09041	-0.177000	0.10690	0.528000	0.53228	AGA			0.498	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000280556.3			
BIRC8	112401	bcgsc.ca	37	19	53792954	53792955	+	Missense_Mutation	DNP	GC	GC	AT	rs35700345|rs34683072|rs386810666	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	GC	GC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:53792954_53792955GC>AT	ENST00000426466.1	-	1	1920_1921	c.673_674GC>AT	c.(673-675)GCg>ATg	p.A225M		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	225			A -> T (in dbSNP:rs35700345).|A -> V (in dbSNP:rs34683072).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		ATCAATAACCGCGCTGCACATG	0.401																																					p.A225M													.	BIRC8	54		0			c.G673A																																									SO:0001583	missense	112401	exon1			ATAACCGCGCTGC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.673_674delinsAT	19.37:g.53792954_53792955delinsAT	ENSP00000412957:p.Ala225Met		182	0	0		199	0.06	11	NM_033341	0		0	Q6IPY1|Q96RW5	Missense_Mutation	DNP	ENST00000426466.1	37	CCDS12863.1																																																																																					0.401	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000464357.1		NM_033341	
VN1R6P	653753	bcgsc.ca	37	19	53818603	53818603	+	IGR	SNP	G	G	A	rs10439122	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:53818603G>A								FAM90A28P (6706 upstream) : ZNF845 (18398 downstream)																							AGCTTTTGGGGTTAGATATTT	0.468													g|||	1213	0.242212	0.2746	0.219	5008	,	,		18923	0.1766		0.3091	False		,,,				2504	0.2137				.													.	.			0			.																																									SO:0001628	intergenic_variant	653753	.			TTTGGGGTTAGAT																													19.37:g.53818603G>A			153	0	0		153	0.08	12	.	0		0		RNA	SNP		37																																																																																					0	0.468										
RDH13	112724	ucsc.edu;bcgsc.ca	37	19	55568084	55568085	+	Missense_Mutation	DNP	CG	CG	TT	rs12608979|rs12609004|rs36097401	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CG	CG					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr19:55568084_55568085CG>TT	ENST00000415061.3	-	3	419_420	c.276_277CG>AA	c.(274-279)aaCGcc>aaAAcc	p.92_93NA>KT	CTC-550B14.6_ENST00000585492.1_RNA|RDH13_ENST00000396247.3_Missense_Mutation_p.21_22NA>KT	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	92					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)	p.N21N(1)		endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	AGGTGCCGGGCGTTGACATGGT	0.564																																					p.NA92KT													RDH13_ENST00000415061,colon,carcinoma,-1,5	RDH13	43	5	1	Substitution - coding silent(1)	large_intestine(1)	c.C276A																																									SO:0001583	missense	112724	exon3			GCCGGGCGTTGAC		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19978	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 3"""		"""retinol dehydrogenase 13 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.276_277delinsTT	19.37:g.55568084_55568085delinsTT	ENSP00000391121:p.N92_A93delinsKT		167	0.0119760479	2		171	0.09	16	NM_001145971	26	0.00	0	Q6UX79|Q96G88	Missense_Mutation	DNP	ENST00000415061.3	37	CCDS54320.1																																																																																					0.564	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000451470.1		NM_138412	
MATN3	4148	broad.mit.edu	37	2	20194085	20194085	+	Frame_Shift_Del	DEL	C	C	-	rs368657984		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:20194085delC	ENST00000407540.3	-	7	1442	c.1380delG	c.(1378-1380)tcgfs	p.S460fs	MATN3_ENST00000421259.2_Frame_Shift_Del_p.S418fs|AC079145.4_ENST00000416575.1_RNA	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	460					extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTGAAGATACGAGCTGACCT	0.458																																					p.S460fs													.	MATN3	28		0			c.1380delG												92.0	91.0	91.0					2																	20194085		1972	4156	6128	SO:0001589	frameshift_variant	4148	exon7			AAGATACGAGCTG	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.1380delG	2.37:g.20194085delC	ENSP00000383894:p.Ser460fs		173	0	0		151	0.01	1	NM_002381	1	0.00	0	B2CPU0|Q4ZG02	Frame_Shift_Del	DEL	ENST00000407540.3	37	CCDS46226.1																																																																																					0.458	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000323925.1		NM_002381	
AFTPH	54812	broad.mit.edu	37	2	64800144	64800144	+	Frame_Shift_Del	DEL	T	T	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:64800144delT	ENST00000422803.1	+	6	2650	c.2336delT	c.(2335-2337)atcfs	p.I779fs	AFTPH_ENST00000487769.1_3'UTR|AFTPH_ENST00000238856.4_Frame_Shift_Del_p.I779fs|AFTPH_ENST00000238855.7_Frame_Shift_Del_p.I779fs|AFTPH_ENST00000409933.1_Frame_Shift_Del_p.I779fs|AFTPH_ENST00000409183.1_Frame_Shift_Del_p.I410fs			Q6ULP2	AFTIN_HUMAN	aftiphilin	779					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						ATAGCTTCCATCGGTCAGACA	0.403																																					p.I779fs													.	AFTPH	117		0			c.2336delT												158.0	159.0	159.0					2																	64800144		2203	4300	6503	SO:0001589	frameshift_variant	54812	exon6			CTTCCATCGGTCA	AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.2336delT	2.37:g.64800144delT	ENSP00000397726:p.Ile779fs		337	0	0		278	0.03	7	NM_017657	95	0.00	0	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Frame_Shift_Del	DEL	ENST00000422803.1	37																																																																																						0.403	AFTPH-202	KNOWN	basic	protein_coding	protein_coding				NM_017657	
WDR92	116143	bcgsc.ca	37	2	68352515	68352515	+	5'UTR	SNP	A	A	C	rs6742154	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:68352515A>C	ENST00000492039.2	-	0	1025							Q96MX6	WDR92_HUMAN	WD repeat domain 92						apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)			endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						TGCTCTGAGCACTGGAGAGAA	0.478													A|||	2202	0.439696	0.2368	0.4352	5008	,	,		21447	0.498		0.4344	False		,,,				2504	0.6626				.													.	.			0			.							A		534,1218		82,370,424	219.0	200.0	206.0			0.2	0.3	2	dbSNP_116	206	1649,2333		360,929,702	no	intergenic				442,1299,1126	CC,CA,AA		41.4114,30.4795,38.0712			68352515	2183,3551	876	1991	2867	SO:0001623	5_prime_UTR_variant	116143	.			CTGAGCACTGGAG	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"""WD repeat domain containing"""	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000492039.2:c.-255T>G	2.37:g.68352515A>C			79	0	0		74	0.09	7	.	0		0	Q96CR6	RNA	SNP	ENST00000492039.2	37																																																																																						0.478	WDR92-002	KNOWN	basic	processed_transcript	protein_coding		OTTHUMT00000326397.3		NM_138458	
LOC285074	285074	bcgsc.ca	37	2	87303060	87303060	+	IGR	SNP	C	C	G	rs62144417	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:87303060C>G								PLGLB1 (54085 upstream) : MIR4771-2 (118848 downstream)																							TGCAGGATCTCGTGCTTGAGA	0.731													.|||	1471	0.29373	0.0756	0.2205	5008	,	,		7949	0.4613		0.3688	False		,,,				2504	0.3906				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGATCTCGTGCTT																													2.37:g.87303060C>G			30	0	0		26	0.15	4	.	8	0.00	0		RNA	SNP		37																																																																																					0	0.731										
Unknown	0	bcgsc.ca	37	2	87355925	87355925	+	IGR	SNP	G	G	A	rs77851313	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:87355925G>A								PLGLB1 (106950 upstream) : MIR4771-2 (65983 downstream)																							TGAACTTCTCGTTCAGTTGGC	0.383																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTTCTCGTTCAGT																													2.37:g.87355925G>A			355	0	0		289	0.06	16	.	0		0		RNA	SNP		37																																																																																					0	0.383										
IGKV1-27	28935	bcgsc.ca	37	2	89513365	89513365	+	RNA	SNP	A	A	G	rs181706250	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:89513365A>G	ENST00000498435.1	-	0	48									immunoglobulin kappa variable 1-27																		GGAGCTGAGCAGGGACCCTCA	0.517													N|||	204	0.0407348	0.0023	0.0663	5008	,	,		14926	0.0		0.0994	False		,,,				2504	0.0562				.													.	.			0			.							T		81,3707		6,69,1819	82.0	80.0	81.0			-5.6	0.0	2		81	785,7439		54,677,3381	no	intergenic				60,746,5200	GG,GA,AA		9.5452,2.1383,7.2095			89513365	866,11146	1894	4112	6006			28935	.			CTGAGCAGGGACC	X63398		2p11.2	2012-02-10			ENSG00000244575	ENSG00000244575		"""Immunoglobulins / IGK locus"""	5735	other	immunoglobulin gene							Standard	NG_000834		Approved	IGKV127, A20			OTTHUMG00000151640		2.37:g.89513365A>G			200	0.015	3		157	0.06	9	.	246	0.00	1		RNA	SNP	ENST00000498435.1	37																																																																																						0.517	IGKV1-27-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene		OTTHUMT00000323389.1		NG_000834	
SNRNP200	23020	hgsc.bcm.edu	37	2	96940775	96940775	+	Missense_Mutation	SNP	G	G	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:96940775G>C	ENST00000323853.5	-	45	6463	c.6386C>G	c.(6385-6387)gCt>gGt	p.A2129G	SNRNP200_ENST00000349783.5_Missense_Mutation_p.A618G	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	2129					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GTCTGTCTCAGCTTCTTTCAC	0.468																																					p.A2129G													.	.			0			c.C6386G												176.0	160.0	165.0					2																	96940775		2203	4300	6503	SO:0001583	missense	23020	exon45			GTCTCAGCTTCTT	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.6386C>G	2.37:g.96940775G>C	ENSP00000317123:p.Ala2129Gly		127	0	0		99	0.05	5	NM_014014	1354	0.00	1	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	.	.	.	.	.	.	.	.	.	.	G	9.620	1.133558	0.21041	.	.	ENSG00000144028	ENST00000323853;ENST00000349783;ENST00000536601;ENST00000543553	T;T	0.68331	-0.32;1.47	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.51534	0.1680	L	0.28400	0.85	0.36555	D	0.872088	B	0.02656	0.0	B	0.01281	0.0	T	0.51919	-0.8644	10	0.02654	T	1	-11.397	16.5621	0.84569	0.0:0.0:1.0:0.0	.	2129	O75643	U520_HUMAN	G	2129;618;588;712	ENSP00000317123:A2129G;ENSP00000326937:A618G	ENSP00000317123:A2129G	A	-	2	0	SNRNP200	96304502	1.000000	0.71417	0.982000	0.44146	0.994000	0.84299	9.525000	0.98039	2.489000	0.83994	0.650000	0.86243	GCT			0.468	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252846.2		NM_014014	
TRIM43CP	643445	bcgsc.ca	37	2	97695036	97695036	+	IGR	SNP	C	C	A	rs116171118	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:97695036C>A								FAM178B (10861 upstream) : FAHD2B (54283 downstream)																							CCATTTTGACCCAGCTTCTCT	0.398													c|||	241	0.048123	0.034	0.0807	5008	,	,		20630	0.0		0.1064	False		,,,				2504	0.0337				.													.	.			0			.																																									SO:0001628	intergenic_variant	643445	.			TTTGACCCAGCTT																													2.37:g.97695036C>A			297	0.0067340067	2		246	0.05	12	.	0		0		RNA	SNP		37																																																																																					0	0.398										
CD8BP	927	bcgsc.ca	37	2	107107511	107107511	+	RNA	SNP	C	C	T	rs11124115	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:107107511C>T	ENST00000416057.1	+	0	223							A6NJW9	CD8BL_HUMAN	CD8b molecule pseudogene						immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											TCTGGGATTCCGCAAAAGGGA	0.537													C|||	1772	0.353834	0.1029	0.3401	5008	,	,		21141	0.7927		0.1869	False		,,,				2504	0.4223				.													.	.			0			.																																											0	.			GGATTCCGCAAAA			2q12.2	2012-10-03	2006-03-28	2006-03-09	ENSG00000254126	ENSG00000254126			1708	pseudogene	pseudogene			"""CD8 antigen, beta polypeptide 2, pseudogene (p37)"""	CD8B2		1541829	Standard	NG_002423		Approved			A6NJW9	OTTHUMG00000153183		2.37:g.107107511C>T			221	0.0090497738	2		193	0.08	16	.	1	0.00	0		RNA	SNP	ENST00000416057.1	37																																																																																						0.537	CD8BP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331218.1		XM_166000	
CD8BP	927	bcgsc.ca	37	2	107107567	107107567	+	RNA	SNP	G	G	C	rs2228021	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:107107567G>C	ENST00000416057.1	+	0	279							A6NJW9	CD8BL_HUMAN	CD8b molecule pseudogene						immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											GCTGTGTTTCGGGATGCAAGC	0.557													G|||	3673	0.733427	0.4917	0.7248	5008	,	,		21896	0.9921		0.6481	False		,,,				2504	0.8875				.													.	.			0			.																																											0	.			TGTTTCGGGATGC			2q12.2	2012-10-03	2006-03-28	2006-03-09	ENSG00000254126	ENSG00000254126			1708	pseudogene	pseudogene			"""CD8 antigen, beta polypeptide 2, pseudogene (p37)"""	CD8B2		1541829	Standard	NG_002423		Approved			A6NJW9	OTTHUMG00000153183		2.37:g.107107567G>C			191	0	0		179	0.08	14	.	5	0.00	0		RNA	SNP	ENST00000416057.1	37																																																																																						0.557	CD8BP-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000331218.1		XM_166000	
NEB	4703	broad.mit.edu	37	2	152364618	152364619	+	Frame_Shift_Ins	INS	-	-	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:152364618_152364619insT	ENST00000172853.10	-	134	18395_18396	c.18248_18249insA	c.(18247-18249)aagfs	p.K6083fs	NEB_ENST00000604864.1_Frame_Shift_Ins_p.K7784fs|NEB_ENST00000409198.1_Frame_Shift_Ins_p.K6083fs|NEB_ENST00000509223.2_5'Flank|NEB_ENST00000427231.2_Frame_Shift_Ins_p.K7784fs|NEB_ENST00000603639.1_Frame_Shift_Ins_p.K7784fs|NEB_ENST00000397345.3_Frame_Shift_Ins_p.K7784fs|NEB_ENST00000498015.2_5'Flank			P20929	NEBU_HUMAN	nebulin	6083					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CTTCCTTGTACTTTTTCTGGGA	0.45																																					p.K7819fs													.	NEB	1697		0			c.23457_23458insA																																									SO:0001589	frameshift_variant	4703	exon163			CTTGTACTTTTTC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18249dupA	2.37:g.152364623_152364623dupT	ENSP00000172853:p.Lys6083fs		171	0	0		163	0.05	8	NM_001271208	22	0.00	0	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Frame_Shift_Ins	INS	ENST00000172853.10	37																																																																																						0.450	NEB-201	KNOWN	basic	protein_coding	protein_coding				NM_004543	
NOSTRIN	115677	broad.mit.edu	37	2	169699562	169699563	+	Frame_Shift_Ins	INS	-	-	A	rs201453794		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:169699562_169699563insA	ENST00000317647.7	+	8	794_795	c.565_566insA	c.(565-567)caafs	p.Q189fs	NOSTRIN_ENST00000445023.2_Frame_Shift_Ins_p.Q111fs|NOSTRIN_ENST00000397209.2_Frame_Shift_Ins_p.Q161fs|NOSTRIN_ENST00000444448.2_Frame_Shift_Ins_p.Q189fs|NOSTRIN_ENST00000458381.2_Frame_Shift_Ins_p.Q189fs|NOSTRIN_ENST00000421711.2_Frame_Shift_Ins_p.Q161fs|NOSTRIN_ENST00000397206.2_Frame_Shift_Ins_p.Q111fs	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	189					endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						AAATTACTACCAAAAAAACATG	0.332																																					p.Q189fs													.	NOSTRIN	68		0			c.565_566insA																																									SO:0001589	frameshift_variant	115677	exon8			TACTACCAAAAAA	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"""nitric oxide synthase trafficker"""			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.572dupA	2.37:g.169699569_169699569dupA	ENSP00000318921:p.Gln189fs		495	0	0		408	0.00	0	NM_001039724	18	0.00	0	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Frame_Shift_Ins	INS	ENST00000317647.7	37	CCDS42771.1																																																																																					0.332	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000333356.4		NM_052946	
CACYBPP2	644877	bcgsc.ca	37	2	184472711	184472711	+	IGR	SNP	T	T	G	rs61733051	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:184472711T>G								RP11-438L19.1 (392583 upstream) : AC093639.1 (296544 downstream)																							TTCTGCGATTTCTGTTGCAAC	0.418													T|||	76	0.0151757	0.0015	0.0159	5008	,	,		20247	0.0		0.0318	False		,,,				2504	0.0317				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCGATTTCTGTTG																													2.37:g.184472711T>G			194	0	0		170	0.05	8	.	16	0.00	0		RNA	SNP		37																																																																																					0	0.418										
KIAA2012	100652824	bcgsc.ca;mdanderson.org	37	2	202939654	202939654	+	Missense_Mutation	SNP	T	T	C	rs10221698	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:202939654T>C	ENST00000541917.1	+	2	498	c.125T>C	c.(124-126)gTc>gCc	p.V42A	AC079354.1_ENST00000409515.3_3'UTR|AC079354.1_ENST00000295844.3_Missense_Mutation_p.V42A																							TATGTTCCTGTCAGCAAACCT	0.468													T|||	1688	0.337061	0.3086	0.4409	5008	,	,		18283	0.2192		0.5298	False		,,,				2504	0.2249				.													.	.			0			.																																									SO:0001583	missense	0	.			TTCCTGTCAGCAA																												ENST00000541917.1:c.125T>C	2.37:g.202939654T>C	ENSP00000437957:p.Val42Ala		220	0.0045454545	1		155	0.06	10	.	0		0		Missense_Mutation	SNP	ENST00000541917.1	37		834	0.38186813186813184	158	0.32113821138211385	159	0.43922651933701656	118	0.2062937062937063	399	0.5263852242744064	T	2.704	-0.270220	0.05716	.	.	ENSG00000182329	ENST00000541917;ENST00000295844	.	.	.	5.93	0.893	0.19236	.	0.147317	0.31859	N	0.006957	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.18863	0.031	B	0.23018	0.043	T	0.46582	-0.9181	8	0.32370	T	0.25	-9.8423	5.7775	0.18287	0.1181:0.3341:0.0:0.5478	rs10221698;rs52811866;rs59419953;rs10221698	42	E7EP55	.	A	42	.	ENSP00000295844:V42A	V	+	2	0	AC079354.1	202647899	0.007000	0.16637	0.836000	0.33094	0.001000	0.01503	1.242000	0.32755	-0.064000	0.13043	-0.274000	0.10170	GTC			0.468	AC079354.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
CPS1	1373	hgsc.bcm.edu	37	2	211459325	211459325	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:211459325G>T	ENST00000233072.5	+	12	1454	c.1258G>T	c.(1258-1260)Gtt>Ttt	p.V420F	CPS1_ENST00000451903.2_5'UTR|CPS1_ENST00000430249.2_Missense_Mutation_p.V426F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	420					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TGCATCTCGGGTTGAGGTCAG	0.373																																					p.V426F													.	.			0			c.G1276T												124.0	113.0	116.0					2																	211459325		2203	4300	6503	SO:0001583	missense	1373	exon13			TCTCGGGTTGAGG	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1258G>T	2.37:g.211459325G>T	ENSP00000233072:p.Val420Phe		110	0	0		96	0.05	5	NM_001122633	1	0.00	0	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.100015	0.37048	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000536125	D;D	0.95069	-3.6;-3.6	5.83	2.27	0.28462	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);	0.472195	0.24287	N	0.039859	D	0.91626	0.7354	M	0.62016	1.91	0.80722	D	1	B;B	0.17038	0.02;0.02	B;B	0.17722	0.019;0.019	D	0.87333	0.2326	10	0.52906	T	0.07	-3.845	8.7229	0.34452	0.4077:0.0:0.5923:0.0	.	430;420	Q59HF8;P31327	.;CPSM_HUMAN	F	426;428;420;420	ENSP00000402608:V426F;ENSP00000233072:V420F	ENSP00000233072:V420F	V	+	1	0	CPS1	211167570	0.993000	0.37304	0.999000	0.59377	0.860000	0.49131	0.304000	0.19228	0.616000	0.30141	0.585000	0.79938	GTT			0.373	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256569.5			
MROH2A	339766	bcgsc.ca;mdanderson.org	37	2	234717839	234717839	+	Missense_Mutation	SNP	C	C	A	rs188948269	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:234717839C>A	ENST00000389758.3	+	22	2529	c.2363C>A	c.(2362-2364)tCc>tAc	p.S788Y				A6NES4	MRO2A_HUMAN	maestro heat-like repeat family member 2A	818																	TGCGTGGCCTCCTACTGCCAC	0.562													C|||	3	0.000599042	0.0	0.0	5008	,	,		18683	0.0		0.003	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001583	missense	339766	.			TGGCCTCCTACTG		CCDS74674.1	2q37.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000185038	ENSG00000185038		"""maestro heat-like repeat containing"""	27936	protein-coding gene	gene with protein product			"""HEAT repeat containing 7B1"""	HEATR7B1		12477932	Standard	NM_001287395		Approved			A6NES4	OTTHUMG00000059037	ENST00000389758.3:c.2363C>A	2.37:g.234717839C>A	ENSP00000374408:p.Ser788Tyr		196	0.0051020408	1		140	0.09	13	.	0		0		Missense_Mutation	SNP	ENST00000389758.3	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	17.78	3.474553	0.63737	.	.	ENSG00000185038	ENST00000389758	T	0.66815	-0.23	5.7	3.9	0.45041	.	0.575228	0.14561	N	0.312068	T	0.58075	0.2097	L	0.57536	1.79	0.23784	N	0.996851	.	.	.	.	.	.	T	0.51498	-0.8698	8	0.30854	T	0.27	.	8.6584	0.34077	0.0:0.8244:0.0:0.1756	.	.	.	.	Y	788	ENSP00000374408:S788Y	ENSP00000374408:S788Y	S	+	2	0	HEATR7B1	234382578	0.002000	0.14202	0.922000	0.36590	0.994000	0.84299	0.187000	0.16998	0.754000	0.32968	0.603000	0.83216	TCC			0.562	MROH2A-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000130646.6		XM_291007	
AC079612.1	0	bcgsc.ca;mdanderson.org	37	2	240500173	240500173	+	Silent	SNP	T	T	C	rs10187580	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:240500173T>C	ENST00000358775.1	+	1	179	c.54T>C	c.(52-54)tcT>tcC	p.S18S															p.S18S(1)		central_nervous_system(1)|pancreas(1)|stomach(2)	4						ccctgtcgtctgcaagctgga	0.557													T|||	1650	0.329473	0.2693	0.3458	5008	,	,		18391	0.1756		0.5	False		,,,				2504	0.3824				.													AC079612.1,NS,carcinoma,0,1	.		1	1	Substitution - coding silent(1)	stomach(1)	.							T		368,1016		48,272,372	62.0	66.0	65.0			-0.7	0.0	2	dbSNP_119	65	1640,1542		427,786,378	no	intergenic				475,1058,750	CC,CT,TT		48.4601,26.5896,43.9772			240500173	2008,2558	692	1591	2283	SO:0001819	synonymous_variant	0	.			GTCGTCTGCAAGC																												ENST00000358775.1:c.54T>C	2.37:g.240500173T>C			90	0.0111111111	1		75	0.09	7	.	0		0		Silent	SNP	ENST00000358775.1	37																																																																																						0.557	AC079612.1-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000257175.2			
CROCC2	728763	bcgsc.ca	37	2	241865156	241865156	+	Silent	SNP	T	T	C	rs4675847	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:241865156T>C	ENST00000430980.2	+	2	93	c.93T>C	c.(91-93)tgT>tgC	p.C31C																								CCGGCCTCTGTCAGGTGAACG	0.647													C|||	3955	0.789736	0.941	0.7478	5008	,	,		17693	0.8889		0.6769	False		,,,				2504	0.6288				.													.	.			0			.																																									SO:0001819	synonymous_variant	0	.			CCTCTGTCAGGTG																												ENST00000430980.2:c.93T>C	2.37:g.241865156T>C			353	0	0		351	0.04	15	.	0		0		Silent	SNP	ENST00000430980.2	37		1768	0.8095238095238095	466	0.9471544715447154	258	0.712707182320442	513	0.8968531468531469	531	0.7005277044854882	C	0.764	-0.768120	0.02974	.	.	ENSG00000226321	ENST00000427156	.	.	.	4.3	-1.11	0.09840	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.18555	-1.0333	3	.	.	.	.	0.7924	0.01060	0.2241:0.3346:0.22:0.2213	rs4675847;rs4675847	.	.	.	P	123	.	.	S	+	1	0	AC104809.3	241513829	0.000000	0.05858	0.175000	0.22980	0.012000	0.07955	-1.659000	0.01975	-0.636000	0.05524	-0.964000	0.02622	TCA			0.647	AC104809.3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding					
CROCC2	728763	bcgsc.ca	37	2	241871956	241871956	+	Intron	SNP	G	G	T	rs12472087	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:241871956G>T	ENST00000430980.2	+	6	726																											GGTCCCTGCAGTGCACTTTGA	0.662													G|||	1923	0.383986	0.1846	0.4352	5008	,	,		17254	0.495		0.4642	False		,,,				2504	0.4202				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CCTGCAGTGCACT																												ENST00000430980.2:c.726+44G>T	2.37:g.241871956G>T			92	0.0108695652	1		73	0.07	5	.	0		0		RNA	SNP	ENST00000430980.2	37																																																																																						0.662	AC104809.3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding					
CROCC2	728763	bcgsc.ca;mdanderson.org	37	2	241872597	241872597	+	Missense_Mutation	SNP	A	A	G	rs4441463	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr2:241872597A>G	ENST00000430980.2	+	8	983	c.983A>G	c.(982-984)cAg>cGg	p.Q328R																								GCCAGTCTCCAGGAGCAGCTG	0.677													a|||	3400	0.678914	0.8018	0.6268	5008	,	,		15969	0.6607		0.664	False		,,,				2504	0.5838				.													.	.			0			.																																									SO:0001583	missense	0	.			GTCTCCAGGAGCA																												ENST00000430980.2:c.983A>G	2.37:g.241872597A>G	ENSP00000387851:p.Gln328Arg		177	0.0169491525	3		136	0.07	10	.	0		0		Missense_Mutation	SNP	ENST00000430980.2	37		1524	0.6978021978021978	398	0.8089430894308943	228	0.6298342541436464	383	0.6695804195804196	515	0.679419525065963	g	0.006	-2.072131	0.00379	.	.	ENSG00000226321	ENST00000430980	T	0.40225	1.04	4.81	-1.89	0.07689	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.36601	-0.9741	5	0.02654	T	1	.	7.7574	0.28932	0.5164:0.1099:0.3736:0.0	rs4441463;rs58128232;rs4441463	.	.	.	R	328	ENSP00000387851:Q328R	ENSP00000387851:Q328R	Q	+	2	0	AC104809.3	241521270	0.002000	0.14202	0.272000	0.24630	0.010000	0.07245	-0.153000	0.10144	-0.798000	0.04444	-1.311000	0.01308	CAG			0.677	AC104809.3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding					
RP11-352D3.2	0	bcgsc.ca;mdanderson.org	37	20	4053254	4053254	+	Missense_Mutation	SNP	A	A	G	rs6139288	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr20:4053254A>G	ENST00000379526.1	-	2	476	c.260T>C	c.(259-261)tTt>tCt	p.F87S																								GAAGAAGGGAAACCAGGCAGG	0.512													A|||	2880	0.57508	0.1248	0.7536	5008	,	,		18933	0.7282		0.6928	False		,,,				2504	0.7781				.													.	.			0			.																																									SO:0001583	missense	0	.			AAGGGAAACCAGG																												ENST00000379526.1:c.260T>C	20.37:g.4053254A>G	ENSP00000368841:p.Phe87Ser		111	0	0		115	0.12	14	.	0		0		Missense_Mutation	SNP	ENST00000379526.1	37		1288	0.5897435897435898	68	0.13821138211382114	268	0.7403314917127072	422	0.7377622377622378	530	0.6992084432717678	A	10.55	1.380271	0.24944	.	.	ENSG00000205300	ENST00000379526	T	0.09911	2.93	2.78	0.504	0.16946	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.08432	-1.0722	5	0.87932	D	0	.	4.5446	0.12074	0.6962:0.0:0.3038:0.0	rs6139288;rs57211523;rs6139288	.	.	.	S	87	ENSP00000368841:F87S	ENSP00000368841:F87S	F	-	2	0	RP11-352D3.2	4001254	0.000000	0.05858	0.000000	0.03702	0.272000	0.26649	-0.005000	0.12855	0.072000	0.16694	0.379000	0.24179	TTT			0.512	RP11-352D3.2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000077799.1			
Unknown	0	bcgsc.ca	37	20	6195664	6195664	+	IGR	SNP	C	C	G	rs3905165	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr20:6195664C>G								FERMT1 (91473 upstream) : AL109618.1 (13776 downstream)																							TATGCCCCCTCCAACAAGAGA	0.383													C|||	1103	0.220248	0.2262	0.2723	5008	,	,		20168	0.119		0.3698	False		,,,				2504	0.1258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCCCCTCCAACAA																													20.37:g.6195664C>G			183	0	0		158	0.06	10	.	5	0.00	0		RNA	SNP		37																																																																																					0	0.383										
NOL4L	140688	hgsc.bcm.edu	37	20	31062436	31062436	+	Missense_Mutation	SNP	C	C	T	rs139591950		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr20:31062436C>T	ENST00000359676.5	-	2	219	c.77G>A	c.(76-78)cGg>cAg	p.R26Q	C20orf112_ENST00000326071.4_Missense_Mutation_p.R26Q|C20orf112_ENST00000375677.1_Missense_Mutation_p.R48Q|C20orf112_ENST00000475781.1_5'UTR|C20orf112_ENST00000375678.3_Missense_Mutation_p.R135Q	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		26						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						CTGCGGGCTCCGCATCCTCTC	0.632																																					p.R270Q													.	.			0			c.G809A							C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	56.0	53.0	54.0		77	5.2	1.0	20	dbSNP_134	54	0,8600		0,0,4300	yes	missense	C20orf112	NM_080616.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	26/437	31062436	1,13005	2203	4300	6503	SO:0001583	missense	140688	exon5			GGGCTCCGCATCC																												ENST00000359676.5:c.77G>A	20.37:g.31062436C>T	ENSP00000352704:p.Arg26Gln		60	0	0		50	0.08	4	NM_001256798	6	0.00	0	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Missense_Mutation	SNP	ENST00000359676.5	37	CCDS13202.1	.	.	.	.	.	.	.	.	.	.	C	17.62	3.435958	0.62955	2.27E-4	0.0	ENSG00000197183	ENST00000359676;ENST00000397984;ENST00000326071;ENST00000375677;ENST00000375678	.	.	.	5.2	5.2	0.72013	.	0.305040	0.30762	N	0.008930	T	0.46658	0.1404	N	0.14661	0.345	0.80722	D	1	D;D	0.67145	0.996;0.994	P;P	0.53912	0.737;0.477	T	0.52253	-0.8600	9	0.87932	D	0	-0.2165	10.898	0.47034	0.0:0.913:0.0:0.087	.	26;26	Q5JYB6;Q96MY1	.;CT112_HUMAN	Q	26;26;26;48;135	.	ENSP00000317413:R26Q	R	-	2	0	C20orf112	30526097	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.831000	0.48144	2.430000	0.82344	0.561000	0.74099	CGG	0		0.632	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000078628.2			
LOC149950	149950	bcgsc.ca	37	20	31189411	31189411	+	5'UTR	SNP	A	A	G	rs2029086	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr20:31189411A>G	ENST00000375670.1	+	0	175				RP11-410N8.4_ENST00000375671.3_5'Flank																							AGGGAGCATGAAGCACCTTGC	0.527													A|||	1718	0.343051	0.1846	0.4006	5008	,	,		19348	0.0804		0.671	False		,,,				2504	0.4499				.													.	.			0			.																																									SO:0001623	5_prime_UTR_variant	0	.			AGCATGAAGCACC																												ENST00000375670.1:c.-58A>G	20.37:g.31189411A>G			93	0.0107526882	1		84	0.08	7	.	0		0		Missense_Mutation	SNP	ENST00000375670.1	37																																																																																						0.527	RP11-410N8.4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000078639.1			
ANKRD20A18P	391269	bcgsc.ca	37	21	15436741	15436741	+	RNA	SNP	C	C	T	rs1810864	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr21:15436741C>T	ENST00000428809.1	+	0	177				AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000448463.1_RNA																							TCCGGCACTCCGAACTGCAGA	0.647													c|||	1265	0.252596	0.0303	0.2608	5008	,	,		10833	0.5149		0.1958	False		,,,				2504	0.3354				.													.	.			0			.																																											391269	.			GCACTCCGAACTG																													21.37:g.15436741C>T			122	0	0		131	0.05	7	.	2	0.00	0		RNA	SNP	ENST00000428809.1	37																																																																																						0.647	AP001347.6-001	KNOWN	basic	antisense	antisense		OTTHUMT00000157812.1			
DGCR6	8214	bcgsc.ca	37	22	18900987	18900987	+	IGR	SNP	G	G	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr22:18900987G>C	ENST00000331444.6	+	0	1214				PRODH_ENST00000357068.6_Missense_Mutation_p.L527V|PRODH_ENST00000420436.1_Missense_Mutation_p.L419V|PRODH_ENST00000334029.2_Missense_Mutation_p.L419V	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6						cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						ATGCCTAGCAGCTGTCCAAAG	0.627																																					p.L527V													.	PRODH	42		0			c.C1579G												81.0	64.0	70.0					22																	18900987		2200	4298	6498	SO:0001628	intergenic_variant	5625	exon14			CTAGCAGCTGTCC	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162		22.37:g.18900987G>C			245	0.0040816327	1		233	0.03	8	NM_016335	3378	0.00	0	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	37	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	N	21.3	4.133011	0.77662	.	.	ENSG00000100033	ENST00000357068;ENST00000313755	T	0.75050	-0.9	4.67	2.58	0.30949	Proline dehydrogenase (1);	0.086607	0.47852	N	0.000206	D	0.88291	0.6397	H	0.95645	3.7	0.48975	D	0.99973	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.87778	0.2610	10	0.87932	D	0	-27.0343	8.7765	0.34765	0.1884:0.0:0.8116:0.0	.	443;527;419	O43272-1;O43272;E7EQL6	.;PROD_HUMAN;.	V	527;172	ENSP00000349577:L527V	ENSP00000318329:L172V	L	-	1	2	PRODH	17280987	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.598000	0.46223	0.520000	0.28426	0.505000	0.49811	CTG			0.627	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000316631.2		NM_005675	
USP41	373856	bcgsc.ca	37	22	20723832	20723832	+	Missense_Mutation	SNP	T	T	C	rs75178771	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr22:20723832T>C	ENST00000454608.2	-	8	513	c.514A>G	c.(514-516)Atg>Gtg	p.M172V	USP41_ENST00000486536.2_5'UTR			Q3LFD5	UBP41_HUMAN	ubiquitin specific peptidase 41	172	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			endometrium(1)|kidney(1)|lung(2)|skin(1)	5						GAGTCCTTCATCCGGATCATA	0.532													T|||	74	0.0147764	0.025	0.0115	5008	,	,		17082	0.0		0.0298	False		,,,				2504	0.0031				.													.	.			0			.																																									SO:0001583	missense	373856	.			CCTTCATCCGGAT	AJ586979		22q11.22	2011-01-31	2005-08-08		ENSG00000161133	ENSG00000161133		"""Ubiquitin-specific peptidases"""	20070	protein-coding gene	gene with protein product			"""ubiquitin specific protease 41"""			12838346	Standard	XM_006710116		Approved		uc011ahq.1	Q3LFD5	OTTHUMG00000151317	ENST00000454608.2:c.514A>G	22.37:g.20723832T>C	ENSP00000414922:p.Met172Val		251	0.0199203187	5		223	0.05	11	.	0		0	A8MXD0|Q70BM7	Missense_Mutation	SNP	ENST00000454608.2	37		64	0.029304029304029304	11	0.022357723577235773	6	0.016574585635359115	6	0.01048951048951049	41	0.05408970976253298	N	0.006	-2.019547	0.00418	.	.	ENSG00000161133	ENST00000454608	T	0.28454	1.61	.	.	.	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.930396	0.09186	N	0.836810	T	0.01421	0.0046	N	0.01464	-0.85	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.32824	-0.9892	7	0.23302	T	0.38	.	.	.	.	.	172	Q3LFD5	UBP41_HUMAN	V	172	ENSP00000414922:M172V	ENSP00000414922:M172V	M	-	1	0	USP41	19053832	0.010000	0.17322	0.425000	0.26659	0.433000	0.31745	-0.916000	0.04029	0.229000	0.21039	0.227000	0.17789	ATG			0.532	USP41-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				XM_036729	
SMPD4P1	645280	bcgsc.ca	37	22	20959252	20959252	+	IGR	SNP	A	A	G	rs526942	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr22:20959252A>G								MED15 (17333 upstream) : SMPD4P1 (11264 downstream)																							CATAGATGTGACTCTTCACAT	0.597													G|||	2168	0.432907	0.6687	0.3098	5008	,	,		19418	0.377		0.2117	False		,,,				2504	0.4867				.													.	.			0			.																																									SO:0001628	intergenic_variant	645280	.			GATGTGACTCTTC																													22.37:g.20959252A>G			34	0	0		62	0.08	5	.	0		0		RNA	SNP		37																																																																																					0	0.597										
Unknown	0	bcgsc.ca	37	22	51193227	51193227	+	IGR	SNP	T	T	G	rs34608236	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr22:51193227T>G								ACR (9465 upstream) : RABL2B (12701 downstream)																							TCAGCCAGAGTTGAAGCATTT	0.493													T|||	347	0.0692891	0.0053	0.1081	5008	,	,		21408	0.0188		0.166	False		,,,				2504	0.0808				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAGAGTTGAAGC																													22.37:g.51193227T>G			212	0.0094339623	2		249	0.08	20	.	120	0.00	0		RNA	SNP		37																																																																																					0	0.493										
DSTNP4	729454	bcgsc.ca	37	3	39255871	39255871	+	IGR	SNP	C	C	G	rs7622622	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:39255871C>G								XIRP1 (21784 upstream) : CX3CR1 (49113 downstream)																							ATTGGTGTAACCATAACTGGT	0.393													C|||	1731	0.345647	0.0567	0.5274	5008	,	,		18873	0.502		0.3439	False		,,,				2504	0.4479				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GTGTAACCATAAC																													3.37:g.39255871C>G			52	0	0		35	0.11	4	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.393										
C3orf84	646498	ucsc.edu;bcgsc.ca;mdanderson.org	37	3	49215966	49215966	+	Silent	SNP	C	C	T	rs9837625	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:49215966C>T	ENST00000545770.2	-	3	233	c.147G>A	c.(145-147)ccG>ccA	p.P49P	C3orf84_ENST00000432035.2_Silent_p.P49P|C3orf84_ENST00000443990.1_5'UTR	NM_001080528.2	NP_001073997.2	H3BNL1	CC084_HUMAN	chromosome 3 open reading frame 84	49																	GTCGCTGCGCCGGCTCCTTGA	0.517													c|||	365	0.0728834	0.084	0.0735	5008	,	,		21868	0.0446		0.1143	False		,,,				2504	0.044				p.P49P													.	.			0			c.G147A									395,3625		14,367,1629	62.0	66.0	65.0		147	-7.2	0.0	3	dbSNP_119	65	900,7474		49,802,3336	no	coding-synonymous	LOC646498	NM_001080528.2		63,1169,4965	TT,TC,CC		10.7476,9.8259,10.4486		49/205	49215966	1295,11099	2010	4187	6197	SO:0001819	synonymous_variant	0	exon3			CTGCGCCGGCTCC		CCDS58831.1	3p21.31	2013-06-21			ENSG00000236980	ENSG00000236980			44666	protein-coding gene	gene with protein product							Standard	NM_001080528		Approved			H3BNL1	OTTHUMG00000156816	ENST00000545770.2:c.147G>A	3.37:g.49215966C>T			68	0	0		57	0.11	6	NM_001080528	0		0		Silent	SNP	ENST00000545770.2	37	CCDS58831.1																																																																																					0.517	C3orf84-002	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000345986.2			
PPATP1	100289640	bcgsc.ca	37	3	87100447	87100447	+	IGR	SNP	G	G	A	rs9831869	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:87100447G>A								VGLL3 (60178 upstream) : MIR4795 (174891 downstream)																							TCATAATATCGTGCTTTTTCT	0.358													G|||	1353	0.270168	0.4032	0.1657	5008	,	,		20276	0.3224		0.1531	False		,,,				2504	0.2311				.													.	.			0			.																																									SO:0001628	intergenic_variant	100289640	.			AATATCGTGCTTT																													3.37:g.87100447G>A			480	0.0020833333	1		358	0.07	25	.	19	0.00	0		RNA	SNP		37																																																																																					0	0.358										
OR5H8	79289	bcgsc.ca	37	3	98031539	98031539	+	lincRNA	SNP	A	A	G	rs2316268	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:98031539A>G	ENST00000508616.1	+	0	149				OR5H8P_ENST00000394191.2_RNA																							ATGTATGTGCACCCTGCATCT	0.408													G|||	2362	0.471645	0.5908	0.428	5008	,	,		16714	0.7312		0.2147	False		,,,				2504	0.3384				.													.	.			0			.																																											79289	.			ATGTGCACCCTGC																													3.37:g.98031539A>G			84	0	0		78	0.05	4	.	0		0		RNA	SNP	ENST00000508616.1	37																																																																																						0.408	RP11-325B23.2-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000359282.1			
WWP1P1	339843	bcgsc.ca	37	3	98377789	98377789	+	IGR	SNP	C	C	G	rs3796137	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:98377789C>G								AC021660.1 (34901 upstream) : ST3GAL6-AS1 (55384 downstream)																							GAGACCACAACCTTTACCTTC	0.438													C|||	1304	0.260383	0.4433	0.2161	5008	,	,		22623	0.2361		0.159	False		,,,				2504	0.1738				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCACAACCTTTAC																													3.37:g.98377789C>G			59	0	0		72	0.15	11	.	0		0		RNA	SNP		37																																																																																					0	0.438										
WWP1P1	339843	bcgsc.ca	37	3	98377862	98377862	+	IGR	SNP	G	G	C	rs3796138	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:98377862G>C								AC021660.1 (34974 upstream) : ST3GAL6-AS1 (55311 downstream)																							AACACCAGAAGAACAACATGG	0.458													C|||	2023	0.403954	0.8684	0.281	5008	,	,		21602	0.2609		0.1978	False		,,,				2504	0.2229				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCAGAAGAACAAC																													3.37:g.98377862G>C			88	0	0		78	0.14	11	.	0		0		RNA	SNP		37																																																																																					0	0.458										
EIF4BP8	339881	bcgsc.ca	37	3	122380614	122380614	+	IGR	SNP	C	C	A	rs790118	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:122380614C>A								PARP15 (22720 upstream) : PARP14 (18850 downstream)																							GAAGTTGCAGCGTCAGCTGGA	0.512													C|||	958	0.191294	0.2716	0.1527	5008	,	,		20120	0.0208		0.2833	False		,,,				2504	0.1912				.													.	.			0			.																																									SO:0001628	intergenic_variant	339881	.			TTGCAGCGTCAGC																													3.37:g.122380614C>A			80	0.0125	1		73	0.12	9	.	0		0		RNA	SNP		37																																																																																					0	0.512										
Unknown	0	bcgsc.ca	37	3	132106634	132106634	+	IGR	SNP	G	G	A	rs10935006	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:132106634G>A								ACPP (19492 upstream) : DNAJC13 (29735 downstream)																							AGTAGCATACGTTATTGAAAA	0.343													G|||	1204	0.240415	0.1263	0.2867	5008	,	,		21679	0.2867		0.2724	False		,,,				2504	0.2812				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GCATACGTTATTG																													3.37:g.132106634G>A			133	0	0		124	0.08	10	.	0		0		RNA	SNP		37																																																																																					0	0.343										
UBQLN4P1	285329	bcgsc.ca	37	3	148703787	148703787	+	IGR	SNP	T	T	G	rs3732559	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:148703787T>G								RP11-680B3.2 (25888 upstream) : GYG1 (5340 downstream)																							AAATCTCACTTCTGACGTCTG	0.547													T|||	2088	0.416933	0.677	0.3429	5008	,	,		20971	0.3641		0.3479	False		,,,				2504	0.2434				.													.	.			0			.																																									SO:0001628	intergenic_variant	285329	.			CTCACTTCTGACG																													3.37:g.148703787T>G			153	0	0		128	0.05	7	.	4	0.00	0		RNA	SNP		37																																																																																					0	0.547										
Unknown	0	bcgsc.ca	37	3	180042256	180042256	+	IGR	SNP	A	A	G	rs9867767	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:180042256A>G								RNA5SP149 (162491 upstream) : RP11-420J11.2 (89705 downstream)																							AACCAAGATTACACAAAAGAT	0.338													G|||	2267	0.452676	0.5522	0.4611	5008	,	,		19912	0.3948		0.336	False		,,,				2504	0.4918				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGATTACACAAA																													3.37:g.180042256A>G			150	0	0		145	0.08	12	.	0		0		RNA	SNP		37																																																																																					0	0.338										
Unknown	0	bcgsc.ca	37	3	180042567	180042567	+	IGR	SNP	A	A	G	rs4854970	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr3:180042567A>G								RNA5SP149 (162802 upstream) : RP11-420J11.2 (89394 downstream)																							ATTTACAGAGACAGAACGAAG	0.517													A|||	1532	0.305911	0.2405	0.3674	5008	,	,		19809	0.3889		0.2346	False		,,,				2504	0.3384				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACAGAGACAGAAC																													3.37:g.180042567A>G			63	0	0		65	0.09	6	.	0		0		RNA	SNP		37																																																																																					0	0.517										
C4orf50	389197	broad.mit.edu;bcgsc.ca	37	4	5990110	5990110	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs4689287	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:5990110C>A	ENST00000324058.5	-	0	56				C4orf50_ENST00000531445.1_Missense_Mutation_p.Q463H			Q6ZRC1	CD050_HUMAN	chromosome 4 open reading frame 50											breast(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(2)|skin(3)|urinary_tract(1)	15						GAGCTTGCCCCTGAGCCACAG	0.547													C|||	1871	0.373602	0.2095	0.3718	5008	,	,		20861	0.6637		0.3161	False		,,,				2504	0.3569				.													.	.			0			.							C		988,3418	368.8+/-318.8	103,782,1318	80.0	74.0	76.0			-5.0	0.0	4	dbSNP_111	76	2760,5840	439.3+/-359.2	459,1842,1999	no	utr-5	C4orf50	XM_003118524.1		562,2624,3317	AA,AC,CC		32.093,22.424,28.8175			5990110	3748,9258	2203	4300	6503			389197	.			TTGCCCCTGAGCC	BC140710		4p16.1	2009-04-14			ENSG00000181215	ENSG00000181215			33766	protein-coding gene	gene with protein product							Standard	XM_003119922		Approved	FLJ46481		Q6ZRC1	OTTHUMG00000149971	ENST00000324058.5:c.-34G>T	4.37:g.5990110C>A			131	0	0		102	0.08	8	.	1	0.00	0		Translation_Start_Site	SNP	ENST00000324058.5	37		879	0.4024725274725275	113	0.22967479674796748	149	0.4116022099447514	381	0.666083916083916	236	0.3113456464379947	C	7.727	0.698398	0.15106	0.22424	0.32093	ENSG00000181215	ENST00000531445	T	0.22945	1.93	4.93	-5.0	0.03001	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.41233	-0.9520	5	0.38643	T	0.18	.	1.3154	0.02106	0.1242:0.2578:0.2526:0.3653	rs4689287;rs61379694;rs4689287	.	.	.	H	463	ENSP00000437121:Q463H	ENSP00000437121:Q463H	Q	-	3	2	C4orf50	6041011	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.466000	0.02355	-0.293000	0.08986	-0.672000	0.03802	CAG			0.547	C4orf50-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				NM_207405	
IGBP1P4	391672	bcgsc.ca	37	4	83323174	83323174	+	RNA	SNP	C	C	T	rs13144673	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:83323174C>T	ENST00000365570.1	-	0	69																											AGATAATATTCACAAACACGC	0.403													C|||	1744	0.348243	0.0688	0.3026	5008	,	,		21912	0.7887		0.3867	False		,,,				2504	0.2648				.													.	.			0			.																																											391672	.			AATATTCACAAAC																													4.37:g.83323174C>T			197	0.0101522843	2		165	0.08	13	.	1	0.00	0		RNA	SNP	ENST00000365570.1	37																																																																																						0.403	SNORD42.2-201	NOVEL	basic	snoRNA	snoRNA					
RPS23P2	391701	bcgsc.ca	37	4	138369443	138369443	+	IGR	SNP	A	A	T	rs9993896	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:138369443A>T								AC060835.1 (220058 upstream) : PCDH18 (70628 downstream)																							CACTAGGAAGAGTGTCAGGGT	0.473													T|||	1346	0.26877	0.5499	0.1326	5008	,	,		18368	0.2381		0.1581	False		,,,				2504	0.1309				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGGAAGAGTGTCA																													4.37:g.138369443A>T			33	0	0		36	0.11	4	.	0		0		RNA	SNP		37																																																																																					0	0.473										
LOC101927636	101927636	bcgsc.ca	37	4	144832823	144832823	+	lincRNA	SNP	T	T	G	rs183478773	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:144832823T>G	ENST00000509873.1	+	0	0																											AACCAGAGTCTCCATTTTCAA	0.408													T|||	15	0.00299521	0.0015	0.0058	5008	,	,		17244	0.001		0.008	False		,,,				2504	0.0				.													.	.			0			.																																											0	.			AGAGTCTCCATTT																													4.37:g.144832823T>G			635	0.0031496063	2		490	0.04	22	.	0		0		RNA	SNP	ENST00000509873.1	37																																																																																						0.408	RP11-673E1.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000364498.1			
LOC101927636	101927636	bcgsc.ca	37	4	144833153	144833154	+	lincRNA	DNP	CT	CT	GG	rs78713560|rs34334789|rs74590858	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CT	CT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:144833153_144833154CT>GG	ENST00000509873.1	+	0	0																											CGTACTTCCCCTGCACCTCGGC	0.554																																					.													.	.			0			.																																											0	.			CTTCCCCTGCACC																												Exception_encountered	4.37:g.144833153_144833154delinsGG			167	0	0		129	0.06	8	.	8	0.00	0		RNA	DNP	ENST00000509873.1	37																																																																																						0.554	RP11-673E1.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000364498.1			
NOL8P1	402191	bcgsc.ca	37	4	166469496	166469496	+	IGR	SNP	G	G	A	rs17587610	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:166469496G>A								CPE (50024 upstream) : RP11-340B18.1 (136294 downstream)																							TCTTCCTAGCGGGTTTCTTTT	0.393													G|||	606	0.121006	0.0053	0.1153	5008	,	,		20256	0.1359		0.167	False		,,,				2504	0.2188				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCTAGCGGGTTTC																													4.37:g.166469496G>A			43	0	0		28	0.14	4	.	0		0		RNA	SNP		37																																																																																					0	0.393										
MORF4	10934	bcgsc.ca;mdanderson.org	37	4	174537356	174537356	+	IGR	SNP	T	T	A	rs34402795	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr4:174537356T>A								RP11-475B2.1 (21649 upstream) : RP11-161D15.2 (280188 downstream)																							TCAAATTTGTTGAGTAGCTGG	0.433													A|||	1528	0.305112	0.3003	0.2723	5008	,	,		20246	0.3244		0.2744	False		,,,				2504	0.3466				.													.	.			0			.							A		1311,3093		210,891,1101	187.0	199.0	194.0			0.5	0.6	4	dbSNP_126	194	2479,6119		382,1715,2202	no	intergenic				592,2606,3303	AA,AT,TT		28.8323,29.7684,29.1494			174537356	3790,9212	2202	4299	6501	SO:0001628	intergenic_variant	10934	.			ATTTGTTGAGTAG																													4.37:g.174537356T>A			183	0	0		148	0.07	11	.	0		0		RNA	SNP		37																																																																																					0	0.433										
TTC37	9652	broad.mit.edu	37	5	94850586	94850587	+	Frame_Shift_Ins	INS	-	-	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr5:94850586_94850587insG	ENST00000358746.2	-	26	2973_2974	c.2675_2676insC	c.(2674-2676)ccafs	p.P892fs	TTC37_ENST00000515176.1_5'UTR	NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	892						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						TTAAATAAGATGGATCAAGGGA	0.307																																					p.P892fs													.	TTC37	128		0			c.2676_2677insC																																									SO:0001589	frameshift_variant	9652	exon26			ATAAGATGGATCA	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.2676dupC	5.37:g.94850588_94850588dupG	ENSP00000351596:p.Pro892fs		510	0	0		360	0.02	7	NM_014639	20	0.00	0	O15077|Q6PJI3	Frame_Shift_Ins	INS	ENST00000358746.2	37	CCDS4072.1																																																																																					0.307	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000241651.1		NM_014639	
RP11-254I22.1	0	broad.mit.edu	37	5	95414786	95414787	+	lincRNA	INS	-	-	TAAAA	rs34328926|rs80243332|rs60523167|rs5869706	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr5:95414786_95414787insTAAAA	ENST00000507997.1	+	0	87				CTD-2337A12.1_ENST00000502645.2_RNA|CTD-2337A12.1_ENST00000511775.1_RNA|MIR583_ENST00000384846.1_RNA																							acccatgcacttaaagttaaaa	0.361														2975	0.59405	0.7156	0.4813	5008	,	,		22499	0.495		0.6362	False		,,,				2504	0.5685				.													.	.			0			.									2353,1165		895,563,301						0.2	0.1		dbSNP_114	36	3841,2837		1367,1107,865	no	intergenic				2262,1670,1166	A1A1,A1R,RR		42.4828,33.1154,39.2507				6194,4002						0	.			ATGCACTTAAAGT																													5.37:g.95414786_95414787insTAAAA			198	0	0		141	0.06	8	.	0		0		RNA	INS	ENST00000507997.1	37																																																																																						0.361	RP11-254I22.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000370578.1			
WDR36	134430	bcgsc.ca	37	5	110436345	110436346	+	Missense_Mutation	DNP	AT	AT	CC	rs145835374|rs142088179	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AT	AT					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr5:110436345_110436346AT>CC	ENST00000513710.2	+	5	639_640	c.635_636AT>CC	c.(634-636)cAT>cCC	p.H212P	WDR36_ENST00000505303.1_Missense_Mutation_p.H156P|WDR36_ENST00000506538.2_Missense_Mutation_p.H212P			Q8NI36	WDR36_HUMAN	WD repeat domain 36	212					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GCAATTTTGCATCCAAGTACCT	0.277																																					p.H212P													.	WDR36	111		0			c.T636C	GRCh37	CX062323	WDR36	X	rs142088179																																				SO:0001583	missense	134430	exon5			TTTTGCATCCAAG	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	Exception_encountered	5.37:g.110436345_110436346delinsCC	ENSP00000424628:p.His212Pro		630	0.0126984127	8		482	0.04	19	NM_139281	3	0.00	0	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	DNP	ENST00000513710.2	37	CCDS4102.1																																																																																					0.277	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		OTTHUMT00000373504.3		NM_139281	
CLINT1	9685	hgsc.bcm.edu;bcgsc.ca	37	5	157233045	157233046	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr5:157233045_157233046delCA	ENST00000411809.2	-	7	974_975	c.770_771delTG	c.(769-771)gtgfs	p.V257fs	CLINT1_ENST00000296951.5_Frame_Shift_Del_p.V239fs|CLINT1_ENST00000523908.1_Frame_Shift_Del_p.V257fs|CLINT1_ENST00000523094.1_Frame_Shift_Del_p.V239fs|CLINT1_ENST00000530742.1_Frame_Shift_Del_p.V239fs	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	257					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCTTTGTCGTCACAGTCTCCTC	0.441																																					p.257_258del	Colon(22;427 587 2170 6147 14291)												.	CLINT1	86		0			c.771_772del																																									SO:0001589	frameshift_variant	9685	exon7			TGTCGTCACAGTC	AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.770_771delTG	5.37:g.157233047_157233048delCA	ENSP00000388340:p.Val257fs		281	0	0		210	0.11	24	NM_014666	39	0.00	0	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Frame_Shift_Del	DEL	ENST00000411809.2	37	CCDS47330.1																																																																																					0.441	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000374001.1		NM_014666	
CDKAL1	54901	bcgsc.ca	37	6	21065449	21065450	+	Missense_Mutation	DNP	CA	CA	TG	rs77152992|rs56087852	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:21065449_21065450CA>TG	ENST00000378610.1	+	10	1236_1237	c.1226_1227CA>TG	c.(1225-1227)cCA>cTG	p.P409L	CDKAL1_ENST00000378624.4_Missense_Mutation_p.P339L|CDKAL1_ENST00000274695.4_Missense_Mutation_p.P409L			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	409					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.P409P(1)|p.P409Q(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			GAACAAGTTCCAGCACAAGTGG	0.391																																					p.P409L													CDKAL1,NS,carcinoma,0,1	CDKAL1	55	1	2	Substitution - Missense(1)|Substitution - coding silent(1)	stomach(1)|lung(1)	c.A1227G																																									SO:0001583	missense	54901	exon12			AAGTTCCAGCACA	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	Exception_encountered	6.37:g.21065449_21065450delinsTG	ENSP00000367873:p.Pro409Leu		140	0	0		120	0.07	8	NM_017774	29	0.00	0	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	DNP	ENST00000378610.1	37	CCDS4546.1																																																																																					0.391	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000039986.1		NM_017774	
BTN2A3P	54718	broad.mit.edu	37	6	26426983	26426984	+	RNA	INS	-	-	T	rs79308421|rs5875109		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:26426983_26426984insT	ENST00000466808.2	+	0	1067							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)											CGAACCTAGTCTTTTTTTTTTT	0.431																																					.													.	.			0			.																																											0	.			CCTAGTCTTTTTT	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26426994_26426994dupT			5	0	0		9	0.33	3	.	0		0	A6NEF4	RNA	INS	ENST00000466808.2	37																																																																																						0.431	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000040118.4		NR_027795	
OR2J4P	442188	bcgsc.ca	37	6	29149561	29149561	+	IGR	SNP	G	G	A	rs3116817	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:29149561G>A								OR2J2 (7210 upstream) : XXbac-BPG308J9.3 (42188 downstream)																							TGGGGTGTGGGAAAGACCATT	0.468													A|||	1894	0.378195	0.112	0.451	5008	,	,		21283	0.378		0.5477	False		,,,				2504	0.5123				.													.	.			0			.																																									SO:0001628	intergenic_variant	442188	.			GTGTGGGAAAGAC																													6.37:g.29149561G>A			115	0	0		100	0.17	17	.	0		0		RNA	SNP		37																																																																																					0	0.468										
OR2J4P	442188	bcgsc.ca	37	6	29149605	29149605	+	IGR	SNP	G	G	T	rs3116818	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:29149605G>T								OR2J2 (7254 upstream) : XXbac-BPG308J9.3 (42144 downstream)																							ACTTTACTTTGTTCTCACACT	0.488													G|||	1586	0.316693	0.0408	0.4035	5008	,	,		21398	0.3512		0.5149	False		,,,				2504	0.3885				.													.	.			0			.																																									SO:0001628	intergenic_variant	442188	.			TACTTTGTTCTCA																													6.37:g.29149605G>T			102	0.0098039216	1		121	0.17	20	.	0		0		RNA	SNP		37																																																																																					0	0.488										
OR2J4P	442188	bcgsc.ca	37	6	29149632	29149632	+	IGR	SNP	T	T	G	rs3129168	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:29149632T>G								OR2J2 (7281 upstream) : XXbac-BPG308J9.3 (42117 downstream)																							CACAGAGTGTTTCCTACTGGT	0.483													G|||	1894	0.378195	0.112	0.451	5008	,	,		21769	0.378		0.5477	False		,,,				2504	0.5123				.													.	.			0			.																																									SO:0001628	intergenic_variant	442188	.			GAGTGTTTCCTAC																													6.37:g.29149632T>G			104	0	0		123	0.17	21	.	0		0		RNA	SNP		37																																																																																					0	0.483										
OR2J4P	442188	bcgsc.ca	37	6	29149645	29149645	+	IGR	SNP	C	C	T	rs3116819	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:29149645C>T								OR2J2 (7294 upstream) : XXbac-BPG308J9.3 (42104 downstream)																							CTACTGGTGGCGATGTCCTAT	0.483													T|||	1894	0.378195	0.112	0.451	5008	,	,		22080	0.378		0.5477	False		,,,				2504	0.5123				.													.	.			0			.																																									SO:0001628	intergenic_variant	442188	.			TGGTGGCGATGTC																													6.37:g.29149645C>T			116	0	0		120	0.15	18	.	0		0		RNA	SNP		37																																																																																					0	0.483										
XXbac-BPG308J9.3	0	bcgsc.ca;mdanderson.org	37	6	29230577	29230577	+	lincRNA	SNP	C	C	A	rs3117328	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:29230577C>A	ENST00000441381.1	+	0	79																											CTCTATATACCTATATCTAAC	0.433													a|||	1806	0.360623	0.1747	0.438	5008	,	,		17855	0.3452		0.5328	False		,,,				2504	0.3957				.													.	.			0			.							A		960,2796		111,738,1029	89.0	78.0	82.0			2.7	0.0	6	dbSNP_103	82	4188,4022		1070,2048,987	no	intergenic				1181,2786,2016	AA,AC,CC		48.989,25.5591,43.0219			29230577	5148,6818	1878	4105	5983			26695	.			ATATACCTATATC																													6.37:g.29230577C>A			106	0	0		87	0.08	7	.	0		0		RNA	SNP	ENST00000441381.1	37																																																																																						0.433	XXbac-BPG308J9.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000192829.1			
PRRT1	80863	broad.mit.edu	37	6	32118387	32118387	+	Missense_Mutation	SNP	G	G	T			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:32118387G>T	ENST00000211413.5	-	2	440	c.316C>A	c.(316-318)Cgc>Agc	p.R106S	PPT2_ENST00000361568.2_5'Flank|PPT2_ENST00000395523.1_5'Flank|PRRT1_ENST00000467780.1_5'Flank|PRRT1_ENST00000375150.2_Intron|PRRT1_ENST00000375152.2_Intron	NM_030651.3	NP_085154.3	Q99946	PRRT1_HUMAN	proline-rich transmembrane protein 1	106					response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						GGTGGCATGCGGGGCAAGGTA	0.796																																					p.R106S													.	PRRT1	14		0			c.C316A												2.0	3.0	2.0					6																	32118387		1047	1952	2999	SO:0001583	missense	80863	exon2			GCATGCGGGGCAA	AK054885	CCDS4739.1	6p21.32	2011-10-10	2005-07-24	2005-07-24		ENSG00000204314		"""Proline-rich transmembrane proteins"""	13943	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 7"""		"""chromosome 6 open reading frame 31"""	C6orf31			Standard	XM_006715221		Approved	NG5, IFITMD7	uc003nzt.3	Q99946		ENST00000211413.5:c.316C>A	6.37:g.32118387G>T	ENSP00000211413:p.Arg106Ser		25	0	0		14	0.14	2	NM_030651	0		0	A6ND08|A6ND40|B0S869|Q5SSW4|Q5SSX7|Q5STI1|Q96DW3|Q96NQ8	Missense_Mutation	SNP	ENST00000211413.5	37	CCDS4739.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067165	0.55539	.	.	ENSG00000204314	ENST00000211413	D	0.91686	-2.89	3.41	3.41	0.39046	.	.	.	.	.	T	0.75781	0.3896	N	0.19112	0.55	0.80722	D	1	B	0.21452	0.056	B	0.10450	0.005	T	0.74719	-0.3570	9	0.48119	T	0.1	.	8.058	0.30617	0.0:0.0:0.7577:0.2423	.	106	Q99946	PRRT1_HUMAN	S	106	ENSP00000211413:R106S	ENSP00000211413:R106S	R	-	1	0	PRRT1	32226365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.209000	0.65208	1.462000	0.47948	0.491000	0.48974	CGC			0.796	PRRT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076255.2		NM_030651	
MYL8P	442204	bcgsc.ca	37	6	33306794	33306794	+	IGR	SNP	T	T	G	rs3130267	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:33306794T>G								DAXX (16003 upstream) : KIFC1 (52518 downstream)																							ACCAAAAAGCTCCCTCAGCGC	0.498													G|||	2873	0.573682	0.7073	0.5476	5008	,	,		20114	0.4157		0.5119	False		,,,				2504	0.638				.													.	.			0			.																																									SO:0001628	intergenic_variant	442204	.			AAAAGCTCCCTCA																													6.37:g.33306794T>G			71	0	0		87	0.07	6	.	0		0		RNA	SNP		37																																																																																					0	0.498										
BDH2P1	389416	bcgsc.ca	37	6	99622711	99622711	+	IGR	SNP	C	C	T	rs13203293	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:99622711C>T								MIR548AI (50139 upstream) : FAXC (96333 downstream)																							AGAGAAGGTGCCAAAGTCATA	0.463													C|||	25	0.00499201	0.0008	0.0029	5008	,	,		16256	0.001		0.0129	False		,,,				2504	0.0082				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGGTGCCAAAGT																													6.37:g.99622711C>T			146	0	0		144	0.06	9	.	0		0		RNA	SNP		37																																																																																					0	0.463										
RP11-557H15.5	0	bcgsc.ca	37	6	134924962	134924962	+	lincRNA	SNP	C	C	T	rs1977140	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr6:134924962C>T	ENST00000412602.1	-	0	958																											CCACCTGCTCCCCAAATGCAA	0.418													C|||	2238	0.446885	0.0393	0.5865	5008	,	,		21551	0.6736		0.5626	False		,,,				2504	0.546				.													.	.			0			.																																											114182	.			CTGCTCCCCAAAT																													6.37:g.134924962C>T			93	0	0		51	0.08	4	.	0		0		RNA	SNP	ENST00000412602.1	37																																																																																						0.418	RP11-557H15.5-001	KNOWN	basic|exp_conf	lincRNA	lincRNA		OTTHUMT00000042327.1			
ELFN1	392617	bcgsc.ca	37	7	1733182	1733182	+	Intron	SNP	C	C	T	rs79496824	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:1733182C>T	ENST00000424383.2	+	1	32				AC074389.7_ENST00000450458.1_lincRNA|AC074389.6_ENST00000382528.1_Missense_Mutation_p.R117H			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						AACACATACACGCCTGTGGAC	0.607													C|||	607	0.121206	0.2057	0.085	5008	,	,		22409	0.0615		0.1103	False		,,,				2504	0.1053				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			CATACACGCCTGT		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+5396C>T	7.37:g.1733182C>T			178	0.0056179775	1		174	0.06	10	.	0		0	H3BS57	Missense_Mutation	SNP	ENST00000424383.2	37	CCDS59046.1	253	0.11584249084249085	97	0.19715447154471544	30	0.08287292817679558	38	0.06643356643356643	88	0.11609498680738786	C	7.926	0.739548	0.15642	.	.	ENSG00000205971	ENST00000382528	.	.	.	1.56	-3.12	0.05282	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.12630	0.006	B	0.04013	0.001	T	0.11251	-1.0595	6	0.87932	D	0	.	6.2046	0.20595	0.0:0.3565:0.0:0.6435	.	117	A2RU56	.	H	117	.	ENSP00000371968:R117H	R	-	2	0	AC074389.6	1699708	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.465000	0.00995	-1.095000	0.03050	-0.671000	0.03813	CGT			0.607	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322893.2		NM_001128636	
ELFN1	392617	bcgsc.ca	37	7	1733192	1733192	+	Intron	SNP	C	C	T	rs56130225	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:1733192C>T	ENST00000424383.2	+	1	32				AC074389.7_ENST00000450458.1_lincRNA|AC074389.6_ENST00000382528.1_Missense_Mutation_p.V114I			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						CGCCTGTGGACGTAGCCTTGC	0.607													c|||	402	0.0802716	0.0613	0.0692	5008	,	,		22447	0.0615		0.1093	False		,,,				2504	0.1033				.													.	.			0			.																																									SO:0001627	intron_variant	0	.			TGTGGACGTAGCC		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+5406C>T	7.37:g.1733192C>T			171	0.0058479532	1		175	0.06	10	.	0		0	H3BS57	Missense_Mutation	SNP	ENST00000424383.2	37	CCDS59046.1	181	0.08287545787545787	31	0.06300813008130081	25	0.06906077348066299	38	0.06643356643356643	87	0.11477572559366754	c	1.460	-0.562701	0.03939	.	.	ENSG00000205971	ENST00000382528	.	.	.	1.3	-2.15	0.07102	.	.	.	.	.	T	0.00637	0.0021	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.08785	-1.0705	6	0.87932	D	0	.	5.1924	0.15216	0.0:0.4116:0.0:0.5884	rs56130225	114	A2RU56	.	I	114	.	ENSP00000371968:V114I	V	-	1	0	AC074389.6	1699718	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-3.315000	0.00515	-0.730000	0.04869	-2.433000	0.00214	GTC			0.607	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000322893.2		NM_001128636	
HSPA8P8	100287551	bcgsc.ca	37	7	10491126	10491126	+	IGR	SNP	C	C	T	rs6970227	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:10491126C>T								U3 (228489 upstream) : AC004535.2 (251176 downstream)																							TGCAATGAACCCCACCAACAC	0.453													C|||	1492	0.297923	0.5129	0.3732	5008	,	,		20437	0.0218		0.3579	False		,,,				2504	0.1769				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATGAACCCCACCA																													7.37:g.10491126C>T			134	0.0074626866	1		126	0.10	12	.	7	0.00	0		RNA	SNP		37																																																																																					0	0.453										
HSPA8P8	100287551	bcgsc.ca	37	7	10492136	10492136	+	IGR	SNP	C	C	T	rs4725276	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:10492136C>T								U3 (229499 upstream) : AC004535.2 (250166 downstream)																							ACTCCTCTTTCCCTTGGTATT	0.458													C|||	949	0.189497	0.2587	0.2839	5008	,	,		22097	0.0218		0.2346	False		,,,				2504	0.1554				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CTCTTTCCCTTGG																													7.37:g.10492136C>T			111	0.018018018	2		100	0.07	7	.	0		0		RNA	SNP		37																																																																																					0	0.458										
Unknown	0	bcgsc.ca	37	7	28319234	28319234	+	IGR	SNP	A	A	C	rs177484	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:28319234A>C								JAZF1-AS1 (35698 upstream) : CREB5 (19705 downstream)																							GTCTTTGGAAACTTTTCTGCA	0.468													A|||	3483	0.695487	0.8585	0.6282	5008	,	,		19807	0.7063		0.5447	False		,,,				2504	0.6667				.													.	.			0			.							A		1116,268		449,218,25	29.0	29.0	29.0			-1.4	0.0	7	dbSNP_79	29	1681,1501		447,787,357	no	intergenic				896,1005,382	CC,CA,AA		47.1716,19.3642,38.7429			28319234	2797,1769	692	1591	2283	SO:0001628	intergenic_variant	0	.			TTGGAAACTTTTC																													7.37:g.28319234A>C			198	0.0050505051	1		202	0.05	10	.	0		0		RNA	SNP		37																																																																																					0	0.468										
CCNJP1	100128459	bcgsc.ca	37	7	56296969	56296969	+	IGR	SNP	C	C	T	rs816390	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:56296969C>T								NUPR1L (112876 upstream) : AC073136.1 (40506 downstream)																							AATCATTGGCCAGCCGTCATG	0.413													C|||	2304	0.460064	0.3366	0.5677	5008	,	,		19021	0.3373		0.6322	False		,,,				2504	0.5				.													.	.			0			.																																									SO:0001628	intergenic_variant	100128459	.			ATTGGCCAGCCGT																													7.37:g.56296969C>T			100	0	0		110	0.06	7	.	0		0		RNA	SNP		37																																																																																					0	0.413										
TNRC18P2	27320	bcgsc.ca	37	7	63040467	63040467	+	IGR	SNP	G	G	A	rs1860493		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:63040467G>A								RP11-340I6.3 (158043 upstream) : RN7SL855P (31355 downstream)																							CTCGGACCACGGTGCCTGGGT	0.537																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	27320	.			GACCACGGTGCCT																													7.37:g.63040467G>A			53	0	0		52	0.12	6	.	0		0		RNA	SNP		37																																																																																					0	0.537										
RP11-340I6.7	0	bcgsc.ca	37	7	63354705	63354705	+	lincRNA	SNP	C	C	A	rs73123056	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:63354705C>A	ENST00000587736.1	-	0	566																											TGAATTTAAGCTAAATCAGCC	0.383													C|||	225	0.0449281	0.0287	0.0836	5008	,	,		19736	0.0		0.0447	False		,,,				2504	0.0859				.													.	.			0			.																																											0	.			TTTAAGCTAAATC																													7.37:g.63354705C>A			222	0	0		257	0.05	14	.	0		0		RNA	SNP	ENST00000587736.1	37																																																																																						0.383	RP11-340I6.7-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000447757.1			
POMZP3	22932	broad.mit.edu	37	7	76247569	76247570	+	Frame_Shift_Ins	INS	-	-	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:76247569_76247570insG	ENST00000310842.4	-	4	959_960	c.275_276insC	c.(274-276)cctfs	p.P92fs	UPK3B_ENST00000443097.2_Intron|UPK3B_ENST00000419923.2_Intron|POMZP3_ENST00000275569.4_Frame_Shift_Ins_p.P92fs|AC004980.7_ENST00000418663.1_RNA	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	92										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				GCCCGGGTCGAGGAACTTTGAA	0.51																																					p.P92fs													.	POMZP3	19		0			c.276_277insC																																									SO:0001589	frameshift_variant	22932	exon4			GGGTCGAGGAACT	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"""POM-ZP3 fusion protein"", ""POM121/ZP3 fusion protein"""	600587	"""POM (POM121 rat homolog) and ZP3 fusion"", ""POM (POM121 homolog, rat) and ZP3 fusion"""			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.276dupC	7.37:g.76247571_76247571dupG	ENSP00000309233:p.Pro92fs		1192	0	0		1742	0.01	12	NM_152992	190	0.00	0	F6STJ3|Q12903|Q9BWB4	Frame_Shift_Ins	INS	ENST00000310842.4	37	CCDS43606.1																																																																																					0.510	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000341775.1		NM_012230	
RP11-274B21.1	0	bcgsc.ca	37	7	128220111	128220111	+	RNA	SNP	G	G	T	rs139965573	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:128220111G>T	ENST00000605862.1	+	0	364																											CCAGTTGCACGATCCTCACCG	0.488													g|||	1657	0.330871	0.1778	0.3098	5008	,	,		16575	0.5635		0.2893	False		,,,				2504	0.3558				.													.	.			0			.																																											0	.			TTGCACGATCCTC																													7.37:g.128220111G>T			822	0.0085158151	7		695	0.04	29	.	8	0.00	0		RNA	SNP	ENST00000605862.1	37																																																																																						0.488	RP11-274B21.1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000468355.1			
CCT8L1P	155100	bcgsc.ca	37	7	152143744	152143744	+	IGR	SNP	A	A	G	rs6953943	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr7:152143744A>G								FABP5P3 (3472 upstream) : LINC01003 (17126 downstream)																							CGTCTACCACAGCATTGATGC	0.552													G|||	2096	0.41853	0.7284	0.3934	5008	,	,		19171	0.2272		0.3678	False		,,,				2504	0.2669				.													.	.			0			.							G		3025,1381	444.9+/-347.5	1050,925,228	50.0	61.0	57.0			4.4	0.1	7	dbSNP_116	57	3098,5502	656.9+/-401.4	585,1928,1787	no	intergenic				1635,2853,2015	GG,GA,AA		36.0233,31.3436,47.0783			152143744	6123,6883	2203	4300	6503	SO:0001628	intergenic_variant	155100	.			TACCACAGCATTG																													7.37:g.152143744A>G			113	0	0		104	0.08	8	.	0		0		RNA	SNP		37																																																																																					0	0.552										
MCM4	4173	hgsc.bcm.edu	37	8	48874151	48874151	+	Missense_Mutation	SNP	A	A	C			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr8:48874151A>C	ENST00000262105.2	+	2	355	c.146A>C	c.(145-147)cAg>cCg	p.Q49P	MCM4_ENST00000523944.1_Missense_Mutation_p.Q49P|PRKDC_ENST00000523565.1_5'Flank|PRKDC_ENST00000314191.2_5'Flank|PRKDC_ENST00000338368.3_5'Flank	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	49					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GGGGAGTTGCAGCCGATGCCA	0.582																																					p.Q49P													.	.			0			c.A146C												87.0	87.0	87.0					8																	48874151		2203	4300	6503	SO:0001583	missense	4173	exon3			AGTTGCAGCCGAT		CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"""MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"""	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.146A>C	8.37:g.48874151A>C	ENSP00000262105:p.Gln49Pro		72	0	0		76	0.11	8	NM_182746	73	0.15	11	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.33|11.33	1.605437|1.605437	0.28623|0.28623	.|.	.|.	ENSG00000104738|ENSG00000104738	ENST00000518221;ENST00000523944;ENST00000262105;ENST00000396826|ENST00000429229	T;T|.	0.02974|.	4.09;4.09|.	5.67|5.67	3.2|3.2	0.36748|0.36748	.|.	0.317261|.	0.35677|.	N|.	0.003041|.	T|T	0.50667|0.50667	0.1629|0.1629	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.25502|0.25502	-1.0130|-1.0130	10|6	0.31617|0.16420	T|T	0.26|0.52	-9.8101|-9.8101	10.0521|10.0521	0.42221|0.42221	0.5968:0.0:0.0:0.4032|0.5968:0.0:0.0:0.4032	.|.	49;49|.	B3KMX0;P33991|.	.;MCM4_HUMAN|.	P|R	49|22	ENSP00000430194:Q49P;ENSP00000262105:Q49P|.	ENSP00000262105:Q49P|ENSP00000400689:S22R	Q|S	+|+	2|1	0|0	MCM4|MCM4	49036704|49036704	0.999000|0.999000	0.42202|0.42202	0.970000|0.970000	0.41538|0.41538	0.046000|0.046000	0.14306|0.14306	1.096000|1.096000	0.30976|0.30976	0.380000|0.380000	0.24823|0.24823	-0.496000|-0.496000	0.04628|0.04628	CAG|AGC			0.582	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000377791.1		NM_005914	
RBMXP2	441391	bcgsc.ca	37	9	30690152	30690152	+	IGR	SNP	C	C	A	rs187211150	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:30690152C>A								snoU13 (511577 upstream) : AL590726.2 (80942 downstream)																							GAGGGCTTACCCCTTCTATGG	0.532													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18890	0.0		0.001	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	441391	.			GCTTACCCCTTCT																													9.37:g.30690152C>A			481	0.0020790021	1		418	0.04	18	.	0		0		RNA	SNP		37																																																																																					0	0.532										
ARMC8P1	100130871	bcgsc.ca	37	9	38453992	38453992	+	IGR	SNP	C	C	T	rs78688365	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:38453992C>T								IGFBPL1 (29548 upstream) : RP11-392E22.12 (86571 downstream)																							CTGAATTGCTCCAGCTGTATA	0.358													C|||	108	0.0215655	0.0023	0.0403	5008	,	,		21857	0.0		0.0636	False		,,,				2504	0.0133				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ATTGCTCCAGCTG																													9.37:g.38453992C>T			22	0	0		19	0.21	4	.	0		0		RNA	SNP		37																																																																																					0	0.358										
Unknown	0	bcgsc.ca	37	9	65632051	65632051	+	IGR	SNP	C	C	T	rs12684652	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:65632051C>T								SPATA31A7 (122441 upstream) : RP11-118H15.1 (248481 downstream)																							GGATCACAGACTTCATCAGGA	0.458													C|||	1023	0.204273	0.1309	0.2104	5008	,	,		14473	0.3065		0.2416	False		,,,				2504	0.1554				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CACAGACTTCATC																													9.37:g.65632051C>T			635	0.0078740157	5		496	0.03	16	.	0		0		RNA	SNP		37																																																																																					0	0.458										
Unknown	0	bcgsc.ca	37	9	88990413	88990413	+	IGR	SNP	C	C	T	rs11141356	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:88990413C>T								ZCCHC6 (21044 upstream) : RP11-359J6.1 (38783 downstream)																							CAGGCGGACACGGCCATGGGT	0.458													C|||	1038	0.207268	0.0703	0.2089	5008	,	,		20531	0.3988		0.1302	False		,,,				2504	0.273				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CGGACACGGCCAT																													9.37:g.88990413C>T			19	0	0		25	0.16	4	.	0		0		RNA	SNP		37																																																																																					0	0.458										
TLK1P1	100129793	bcgsc.ca	37	9	125449495	125449499	+	IGR	DEL	AAAAC	AAAAC	-	rs143799138	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	AAAAC	AAAAC					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:125449495_125449499delAAAAC								OR1L3 (11063 upstream) : OR1L4 (36769 downstream)																							AAACAAAGGAAAAACAAAGGAGTCA	0.371														19	0.00379393	0.0008	0.0101	5008	,	,		22227	0.0		0.0099	False		,,,				2504	0.001				.													.	.			0			.																																									SO:0001628	intergenic_variant	100129793	.			AAAGGAAAAACAA																													9.37:g.125449495_125449499delAAAAC			92	0	0		80	0.05	4	.	0		0		RNA	DEL		37																																																																																					0	0.371										
HMCN2	256158	bcgsc.ca	37	9	133294244	133294244	+	Silent	SNP	G	G	A	rs13294886	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chr9:133294244G>A	ENST00000428715.1	+	2	178	c.177G>A	c.(175-177)gaG>gaA	p.E59E	HMCN2_ENST00000487727.2_3'UTR			Q8NDA2	HMCN2_HUMAN	hemicentin 2	4335	VWFA.				response to stimulus (GO:0050896)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)										CCACTGGAGAGCCCACACCCA	0.677													G|||	1752	0.34984	0.1505	0.3401	5008	,	,		14476	0.3601		0.4771	False		,,,				2504	0.4847				.													.	.			0			.																																									SO:0001819	synonymous_variant	256158	.			TGGAGAGCCCACA	AK074396		9q34.11	2013-01-29			ENSG00000148357	ENSG00000148357		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21293	protein-coding gene	gene with protein product							Standard	XM_006710218		Approved	DKFZp434P0216, FLJ23816		Q8NDA2	OTTHUMG00000140096	ENST00000428715.1:c.177G>A	9.37:g.133294244G>A			195	0.0102564103	2		142	0.05	7	.	1	0.00	0	Q8N225|Q8TCI8	Silent	SNP	ENST00000428715.1	37																																																																																						0.677	HMCN2-001	NOVEL	basic|exp_conf	protein_coding	protein_coding		OTTHUMT00000054661.2		XM_175125	
Unknown	0	bcgsc.ca	37	X	35077823	35077823	+	IGR	SNP	T	T	C	rs3109859	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:35077823T>C								AL596268.1 (3248 upstream) : RNU6-1087P (534466 downstream)																							GGAAAAGTACTTGGAGTACTG	0.458													T|||	2802	0.742252	0.469	0.598	3775	,	,		15891	0.6607		0.5467	False		,,,				2504	0.5634				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AAGTACTTGGAGT																													X.37:g.35077823T>C			35	0	0		43	0.12	5	.	0		0		RNA	SNP		37																																																																																					0	0.458										
SALL1P1	139163	bcgsc.ca	37	X	49431714	49431714	+	IGR	SNP	A	A	G	rs6608906	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:49431714A>G								GAGE1 (60756 upstream) : PAGE1 (20338 downstream)																							GAGGGTTGGGAGCAATGGCAG	0.542													G|||	149	0.0394702	0.0272	0.0231	3775	,	,		13223	0.0476		0.0129	False		,,,				2504	0.0368				.													.	.			0			.																																									SO:0001628	intergenic_variant	139163	.			GTTGGGAGCAATG																													X.37:g.49431714A>G			22	0	0		24	0.21	5	.	0		0		RNA	SNP		37																																																																																					0	0.542										
SALL1P1	139163	bcgsc.ca	37	X	49432879	49432880	+	IGR	DNP	CA	CA	TG	rs147747838|rs181522811		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	CA	CA					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:49432879_49432880CA>TG								GAGE1 (61921 upstream) : PAGE1 (19172 downstream)																							AGGTTGTGATCACTGAGGTATC	0.554																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	139163	.			TGTGATCACTGAG																													X.37:g.49432879_49432880delinsTG			42	0	0		64	0.08	5	.	0		0		RNA	DNP		37																																																																																					0	0.554										
SALL1P1	139163	bcgsc.ca	37	X	49432943	49432943	+	IGR	SNP	T	T	C	rs6608907	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:49432943T>C								GAGE1 (61985 upstream) : PAGE1 (19109 downstream)																							gctgtggctgtggctggaagt	0.562													C||||C|||	146|146	0.0386755|0.0386755	0.025|0.025	0.0231|0.0231	3775|3775	,|,	,|,		12283|12283	0.0476|0.0476		0.0129|0.0129	False|False		,,,|,,,				2504|2504	0.0368|0.0368				.													.	.			0			.																																									SO:0001628	intergenic_variant	139163	.			TGGCTGTGGCTGG																													X.37:g.49432943T>C			36	0	0		42	0.10	4	.	0		0		RNA	SNP		37																																																																																					0	0.562										
Unknown	0	bcgsc.ca	37	X	53834482	53834482	+	IGR	SNP	A	A	C	rs10449002	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:53834482A>C								HUWE1 (120809 upstream) : RNA5SP505 (101005 downstream)																							TTTTGGATTGAAGCTCCCAAA	0.433													C|||	1457	0.38596	0.1619	0.2968	3775	,	,		13098	0.3879		0.3091	False		,,,				2504	0.3425				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGATTGAAGCTCC																													X.37:g.53834482A>C			25	0	0		25	0.20	5	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.433										
SERBP1P1	389866	bcgsc.ca	37	X	68003320	68003320	+	IGR	SNP	T	T	C	rs12012713	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:68003320T>C								STARD8 (57638 upstream) : EFNB1 (45519 downstream)																							CCATCATGCCTGGGCACTTAC	0.607													t|||	345	0.0913907	0.2496	0.0187	3775	,	,		11335	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CATGCCTGGGCAC																													X.37:g.68003320T>C			53	0.0188679245	1		67	0.13	9	.	0		0		RNA	SNP		37																																																																																					0	0.607										
SERBP1P1	389866	bcgsc.ca	37	X	68004148	68004148	+	IGR	SNP	T	T	C	rs7061948	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:68004148T>C								STARD8 (58466 upstream) : EFNB1 (44691 downstream)																							GCGACCACCTTGTGAACGAAG	0.408													N|||	251	0.0664901	0.1815	0.013	3775	,	,		13910	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CCACCTTGTGAAC																													X.37:g.68004148T>C			110	0	0		113	0.11	12	.	0		0		RNA	SNP		37																																																																																					0	0.408										
SERBP1P1	389866	bcgsc.ca	37	X	68004230	68004230	+	IGR	SNP	A	A	C	rs7058210		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:68004230A>C								STARD8 (58548 upstream) : EFNB1 (44609 downstream)																							ATTGACCGACATATTCGAGGT	0.478													C|||	254	0.0672848	0.1838	0.013	3775	,	,		15308	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			ACCGACATATTCG																													X.37:g.68004230A>C			274	0	0		248	0.10	25	.	1	1.00	1		RNA	SNP		37																																																																																					0	0.478										
SERBP1P1	389866	bcgsc.ca	37	X	68004333	68004333	+	IGR	SNP	G	G	T	rs111708563		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:68004333G>T								STARD8 (58651 upstream) : EFNB1 (44506 downstream)																							AATTTGATAGGCATAGTGGAA	0.502													G|||	254	0.0672848	0.1838	0.013	3775	,	,		14968	0.0		0.002	False		,,,				2504	0.0				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGATAGGCATAGT																													X.37:g.68004333G>T			306	0.0065359477	2		302	0.13	39	.	59	0.00	0		RNA	SNP		37																																																																																					0	0.502										
LDHBP2	3947	bcgsc.ca	37	X	75556211	75556211	+	IGR	SNP	C	C	A	rs11798238	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:75556211C>A								RNU6-867P (90738 upstream) : MAGEE1 (91834 downstream)																							TCTTCCGCAACTGGTACAATG	0.448													C|||	277	0.0733775	0.0038	0.0562	3775	,	,		13546	0.0		0.166	False		,,,				2504	0.0675				.													.	.			0			.																																									SO:0001628	intergenic_variant	3947	.			CCGCAACTGGTAC																													X.37:g.75556211C>A			35	0	0		38	0.16	6	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.448										
USP12PX	254700	bcgsc.ca	37	X	89368606	89368606	+	IGR	SNP	G	G	T	rs5941478		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:89368606G>T								TGIF2LX (190724 upstream) : RNU6-555P (483627 downstream)																							ATTATATTGCGATAGTTAAGA	0.398													G||||G|||	932|932	0.246887|0.246887	0.1127|0.1127	0.1888|0.1888	3775|3775	,|,	,|,		13450|13450	0.0109|0.0109		0.4085|0.4085	False|False		,,,|,,,				2504|2504	0.2352|0.2352				.													.	.			0			.																																									SO:0001628	intergenic_variant	254700	.			TATTGCGATAGTT																													X.37:g.89368606G>T			108	0	0		119	0.06	7	.	1	0.00	0		RNA	SNP		37																																																																																					0	0.398										
Unknown	0	bcgsc.ca	37	X	100212525	100212525	+	IGR	SNP	T	T	C	rs6616208	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:100212525T>C								XKRX (28103 upstream) : ARL13A (12174 downstream)																							AAGCTGTTGGTTGAAATCATA	0.458													t|||	2204	0.583841	0.2927	0.4467	3775	,	,		15193	0.6448		0.3797	False		,,,				2504	0.4857				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TGTTGGTTGAAAT																													X.37:g.100212525T>C			52	0	0		54	0.13	7	.	3	0.00	0		RNA	SNP		37																																																																																					0	0.458										
TCP11X3P	106481605	bcgsc.ca	37	X	101437635	101437635	+	RNA	SNP	A	A	G	rs5945049	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:101437635A>G	ENST00000508552.1	+	0	252									t-complex 11 family, X-linked 3, pseudogene																		ATTTATCTCCAGGTAAGATTC	0.383													.|||	522	0.138278	0.0666	0.1354	3775	,	,		15061	0.001		0.2863	False		,,,				2504	0.0521				.													.	.			0			.																																											0	.			ATCTCCAGGTAAG			Xq22.1	2013-05-14			ENSG00000251525	ENSG00000251525			48370	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000022051		X.37:g.101437635A>G			502	0.0059760956	3		433	0.09	39	.	0		0		RNA	SNP	ENST00000508552.1	37																																																																																						0.383	TCP11X3P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000332190.1			
FRMPD3	84443	ucsc.edu;bcgsc.ca;mdanderson.org	37	X	106796084	106796084	+	Silent	SNP	T	T	C	rs12011630	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:106796084T>C	ENST00000276185.4	+	8	669	c.669T>C	c.(667-669)ctT>ctC	p.L223L	FRMPD3_ENST00000477796.1_3'UTR			Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	223	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					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						ACTTTGCTCTTGTCCTTGAGT	0.458													t|||	669	0.177219	0.3971	0.1095	3775	,	,		14784	0.0327		0.005	False		,,,				2504	0.0307				.													.	.			0			.									653,765		119,260,155,163,179	47.0	41.0	42.0		804	-3.5	1.0	X	dbSNP_120	42	20,3087		1,14,4,1101,871	no	coding-synonymous	FRMPD3	XM_042978.7		120,274,159,1264,1050	CC,CT,C,TT,T		0.6437,46.0508,14.8729		268/1856	106796084	673,3852	876	1991	2867	SO:0001819	synonymous_variant	84443	.			TGCTCTTGTCCTT	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.669T>C	X.37:g.106796084T>C			90	0	0		101	0.14	14	.	0		0	Q96JK8	Silent	SNP	ENST00000276185.4	37																																																																																						0.458	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
FRMPD3	84443	ucsc.edu;bcgsc.ca;mdanderson.org	37	X	106841068	106841068	+	Silent	SNP	G	G	A	rs61184704		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:106841068G>A	ENST00000276185.4	+	15	2058	c.2058G>A	c.(2056-2058)gaG>gaA	p.E686E				Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	686	Poly-Glu.					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						aggaggaggaggaggaggaag	0.587													G|||	610	0.161589	0.3404	0.1009	3775	,	,		14104	0.0407		0.004	False		,,,				2504	0.046				.													.	.			0			.							G		560,853		82,257,139,202,192	10.0	10.0	10.0		2193	-2.0	1.0	X	dbSNP_129	10	9,3086		1,5,2,1110,861	no	coding-synonymous	FRMPD3	XM_042978.7		83,262,141,1312,1053	AA,AG,A,GG,G		0.2908,39.632,12.622		731/1856	106841068	569,3939	872	1979	2851	SO:0001819	synonymous_variant	84443	.			GGAGGAGGAGGAG	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.2058G>A	X.37:g.106841068G>A			64	0	0		51	0.16	8	.	0		0	Q96JK8	Silent	SNP	ENST00000276185.4	37																																																																																						0.587	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
NCBP2L	392517	bcgsc.ca	37	X	107037795	107037795	+	Silent	SNP	C	C	A	rs5962885	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:107037795C>A	ENST00000509000.2	+	2	543	c.345C>A	c.(343-345)gtC>gtA	p.V115V	NCBP2L_ENST00000372379.2_Silent_p.V115V			A6PVI3	NCB2L_HUMAN	nuclear cap binding protein subunit 2-like	115	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA cis splicing, via spliceosome (GO:0045292)	nuclear cap binding complex (GO:0005846)	nucleotide binding (GO:0000166)|RNA cap binding (GO:0000339)			large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	5						ATTGGGATGTCGGTTTTAGAG	0.463													A|||	1171	0.310199	0.6006	0.1052	3775	,	,		12995	0.1012		0.1093	False		,,,				2504	0.0941				.													.	.			0			.							A		999,419		262,234,241,46,93	134.0	120.0	124.0			-2.0	0.0	X	dbSNP_114	124	391,2716		23,242,103,851,772	no	intergenic				285,476,344,897,865	AA,AC,A,CC,C		12.5845,29.5487,30.7182			107037795	1390,3135	876	1991	2867	SO:0001819	synonymous_variant	392517	.			GGATGTCGGTTTT			Xq22.3	2013-02-12			ENSG00000170935	ENSG00000170935		"""RNA binding motif (RRM) containing"""	31795	protein-coding gene	gene with protein product							Standard	NG_011409		Approved			A6PVI3	OTTHUMG00000022169	ENST00000509000.2:c.345C>A	X.37:g.107037795C>A			102	0.0098039216	1		147	0.11	16	.	0		0		Silent	SNP	ENST00000509000.2	37																																																																																						0.463	NCBP2L-001	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		OTTHUMT00000057850.2		XM_373362	
EIF4BP7	643873	bcgsc.ca	37	X	110863204	110863204	+	IGR	SNP	A	A	G			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:110863204A>G								RN7SL661P (3803 upstream) : RNA5SP512 (49852 downstream)																							AGCTGGAGCTACTTTTCCCCC	0.507																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	643873	.			GGAGCTACTTTTC																													X.37:g.110863204A>G			50	0	0		62	0.10	6	.	24	0.00	0		RNA	SNP		37																																																																																					0	0.507										
Unknown	0	bcgsc.ca	37	X	114659687	114659687	+	IGR	SNP	A	A	G	rs926705	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:114659687A>G								LUZP4 (117566 upstream) : RP1-93I3.1 (92802 downstream)																							TGAGAGTGGAATTGTAGGGCT	0.453													G|||	483	0.127947	0.0643	0.1484	3775	,	,		14418	0.0407		0.1948	False		,,,				2504	0.0593				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			AGTGGAATTGTAG																													X.37:g.114659687A>G			33	0.0303030303	1		16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.453										
API5P1	642812	bcgsc.ca	37	X	115239675	115239675	+	IGR	SNP	G	G	C	rs7057314	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:115239675G>C								RN7SL712P (130575 upstream) : AGTR2 (62299 downstream)																							GCTCCTCTACGTTCGGCACAG	0.547													C|||	1547	0.409801	0.5401	0.3098	3775	,	,		12755	0.1052		0.3579	False		,,,				2504	0.1554				.													.	.			0			.																																									SO:0001628	intergenic_variant	642812	.			CTCTACGTTCGGC																													X.37:g.115239675G>C			114	0.0087719298	1		101	0.08	8	.	0		0		RNA	SNP		37																																																																																					0	0.547										
LINC01285	101928287	bcgsc.ca	37	X	118012888	118012888	+	IGR	SNP	G	G	A	rs261662	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:118012888G>A								RP4-562J12.2 (21039 upstream) : LONRF3 (95692 downstream)																							AGCCTCTTCAGTGACGTCTCT	0.582													A|||	1559	0.41298	0.4455	0.2637	3775	,	,		12987	0.1657		0.341	False		,,,				2504	0.2832				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TCTTCAGTGACGT																													X.37:g.118012888G>A			49	0	0		73	0.08	6	.	0		0		RNA	SNP		37																																																																																					0	0.582										
Unknown	0	bcgsc.ca	37	X	134345975	134345975	+	IGR	SNP	G	G	A	rs147984738		TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:134345975G>A								AL590282.1 (5398 upstream) : ZNF75D (36891 downstream)																							AGTTTTAATTGGATGTGTTAC	0.353													g|||	22	0.00582781	0.0015	0.0029	3775	,	,		14366	0.0		0.0119	False		,,,				2504	0.0061				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			TTAATTGGATGTG																													X.37:g.134345975G>A			310	0.0032258065	1		317	0.08	24	.	0		0		RNA	SNP		37																																																																																					0	0.353										
SAGE4P	442465	bcgsc.ca	37	X	134741152	134741152	+	IGR	SNP	C	C	T	rs5929670	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:134741152C>T								DDX26B (24718 upstream) : CT45A1 (106032 downstream)																							TTTCCAGATGCTGCAGTCACT	0.478													C|||	3031	0.802914	0.4501	0.6542	3775	,	,		15866	0.6359		0.7247	False		,,,				2504	0.6258				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			CAGATGCTGCAGT																													X.37:g.134741152C>T			158	0.0063291139	1		164	0.10	17	.	0		0		RNA	SNP		37																																																																																					0	0.478										
CT45A11P	100129813	bcgsc.ca	37	X	135027101	135027101	+	IGR	SNP	T	T	C	rs6528321	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:135027101T>C								SAGE1 (31881 upstream) : MMGT1 (17127 downstream)																							CACAGGTGCATTGCTACCAGA	0.418													T|||	3192	0.845563	0.6702	0.6196	3775	,	,		15054	0.6498		0.5875	False		,,,				2504	0.6442				.													.	.			0			.																																									SO:0001628	intergenic_variant	0	.			GGTGCATTGCTAC																													X.37:g.135027101T>C			99	0.0101010101	1		87	0.08	7	.	0		0		RNA	SNP		37																																																																																					0	0.418										
ZFYVE9P1	100289259	bcgsc.ca	37	X	136742802	136742802	+	IGR	SNP	T	T	C	rs4240110	byFrequency	TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:136742802T>C								RN7SL325P (65092 upstream) : RNU6-985P (27247 downstream)																							GATATTCCTCTATTCTCTGGC	0.483													T|||	1692	0.448212	0.2511	0.3833	3775	,	,		15265	0.3016		0.3738	False		,,,				2504	0.4233				.													.	.			0			.																																									SO:0001628	intergenic_variant	100289259	.			TTCCTCTATTCTC																													X.37:g.136742802T>C			65	0.0153846154	1		48	0.10	5	.	0		0		RNA	SNP		37																																																																																					0	0.483										
RP13-228J13.1	0	broad.mit.edu	37	X	154578866	154578866	+	RNA	DEL	T	T	-			TCGA-VF-A8A9-01A-11D-A435-10	TCGA-VF-A8A9-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0612a927-064e-4f49-9539-52c45867c5f6	3891e12d-7570-4058-8227-fdc2c5caa80a	g.chrX:154578866delT	ENST00000412436.1	-	0	98				RP13-228J13.5_ENST00000453508.1_RNA|RP13-228J13.1_ENST00000444722.1_RNA																							TTTCTCTCTGTTTTTTTTTTT	0.418														73	0.0193377	0.0121	0.0086	3775	,	,		10483	0.0139		0.0149	False		,,,				2504	0.0225				.													.	.			0			.																																											0	.			TCTCTGTTTTTTT																													X.37:g.154578866delT			8	0	0		13	0.46	6	.	0		0		RNA	DEL	ENST00000412436.1	37																																																																																						0.418	RP13-228J13.1-001	KNOWN	basic	antisense	antisense		OTTHUMT00000058799.1			
