#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_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
TCEANC	170082	genome.wustl.edu	37	X	13680763	13680763	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chrX:13680763A>G	ENST00000380600.1	+	2	223	c.136A>G	c.(136-138)Aca>Gca	p.T46A	TCEANC_ENST00000544987.1_Missense_Mutation_p.T46A|TCEANC_ENST00000545566.1_Missense_Mutation_p.T46A|TCEANC_ENST00000314720.4_Missense_Mutation_p.T76A|TCEANC_ENST00000490617.1_3'UTR			Q8N8B7	TEANC_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing	46	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|large_intestine(5)|lung(2)|pancreas(1)	9						TCTCCAGGAGACAGATGTGGT	0.423																																						dbGAP											0			X											91.0	85.0	87.0					X																	13680763		1920	4121	6041	13590684	SO:0001583	missense	0				CCDS48081.1, CCDS75954.1	Xp22.2	2009-01-30			ENSG00000176896	ENSG00000176896			28277	protein-coding gene	gene with protein product						12477932	Standard	XM_005274454		Approved	MGC17403	uc010neg.1	Q8N8B7	OTTHUMG00000021154	ENST00000380600.1:c.136A>G	X.37:g.13680763A>G	ENSP00000369974:p.Thr46Ala	Somatic	179	0.00	0		5	0.00	0	WXS	Illumina HiSeq	Phase_IV	13590684	107	34.13	57	A6NI06|B2RDM3	Missense_Mutation	SNP	HMMPfam_TFIIS_M,superfamily_Elongation factor TFIIS domain 2,HMMPfam_TFIIS,superfamily_Conserved domain common to transcription factors TFIIS elongin A CRSP70,HMMSmart_SM00510,superfamily_Zinc beta-ribbon	p.T76A	ENST00000380600.1	37	c.226		X	.	.	.	.	.	.	.	.	.	.	A	21.2	4.115702	0.77323	.	.	ENSG00000176896	ENST00000545566;ENST00000544987;ENST00000314720;ENST00000380600	T;T;T;T	0.62788	0.01;0.01;0.0;0.01	5.28	5.28	0.74379	Transcription factor IIS, N-terminal (4);	0.000000	0.64402	D	0.000001	T	0.71169	0.3308	L	0.36672	1.1	0.46874	D	0.999234	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.74621	-0.3604	10	0.87932	D	0	-6.1435	14.331	0.66556	1.0:0.0:0.0:0.0	.	76;46	Q8N8B7-2;Q8N8B7	.;TEANC_HUMAN	A	46;46;76;46	ENSP00000438952:T46A;ENSP00000440038:T46A;ENSP00000313886:T76A;ENSP00000369974:T46A	ENSP00000313886:T76A	T	+	1	0	TCEANC	13590684	1.000000	0.71417	0.991000	0.47740	0.971000	0.66376	7.564000	0.82326	1.763000	0.52060	0.486000	0.48141	ACA	-	HMMPfam_TFIIS,superfamily_Conserved domain common to transcription factors TFIIS elongin A CRSP70		0.423	TCEANC-002	KNOWN	basic|appris_principal	protein_coding	TCEANC	protein_coding	OTTHUMT00000055796.1	A	NM_152634		13590684	+1	no_errors	NM_152634.2	genbank	human	validated	54_36p	missense	SNP	1.000	G
BCAR3	8412	genome.wustl.edu	37	1	94048128	94048128	+	Silent	SNP	G	G	A			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr1:94048128G>A	ENST00000370244.1	-	9	1704	c.1416C>T	c.(1414-1416)ggC>ggT	p.G472G	BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370247.3_Silent_p.G381G|BCAR3_ENST00000539242.1_Silent_p.G148G|BCAR3_ENST00000370243.1_Silent_p.G472G|BCAR3_ENST00000260502.6_Silent_p.G472G	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	472					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		agtagttgacgccagagttcc	0.582																																						dbGAP											0			1											58.0	49.0	52.0					1																	94048128		2203	4300	6503	93820716	SO:0001819	synonymous_variant	0			U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.1416C>T	1.37:g.94048128G>A		Somatic	150	0.00	0		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	93820716	97	37.58	59	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00147,superfamily_Ras GEF	p.G472	ENST00000370244.1	37	c.1416	CCDS745.1	1																																																																																			-	superfamily_Ras GEF		0.582	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	BCAR3	protein_coding	OTTHUMT00000028420.1	G			93820716	-1	no_errors	NM_003567.2	genbank	human	reviewed	54_36p	silent	SNP	0.782	A
DRD5P1	1817	genome.wustl.edu	37	2	91873695	91873695	+	RNA	SNP	C	C	T			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr2:91873695C>T	ENST00000436174.1	-	0	1145																											CATCTTGGCGCGCAGGTGGCG	0.632																																						dbGAP											0			2																																								91237422			0																															2.37:g.91873695C>T		Somatic	81	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	91237422	61	35.79	34		Missense_Mutation	SNP	HMMPfam_7tm_1,superfamily_SSF81321	p.R72H	ENST00000436174.1	37	c.215		2																																																																																			-	HMMPfam_7tm_1,superfamily_SSF81321		0.632	AC027612.3-002	KNOWN	basic	processed_transcript	DRD5P1	pseudogene	OTTHUMT00000338339.1	C			91237422	-1	no_errors	ENST00000328341	ensembl	human	known	54_36p	missense	SNP	1.000	T
ADCY5	111	genome.wustl.edu	37	3	123071312	123071312	+	Silent	SNP	C	C	T	rs200302997		TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr3:123071312C>T	ENST00000462833.1	-	2	2463	c.1251G>A	c.(1249-1251)gcG>gcA	p.A417A	ADCY5_ENST00000491190.1_Silent_p.A50A|ADCY5_ENST00000309879.5_Silent_p.A67A|ADCY5_ENST00000470367.1_5'UTR	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	417					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		AGTGGAGCCGCGCCTGGATGC	0.617																																						dbGAP											0			3											56.0	56.0	56.0					3																	123071312		2203	4300	6503	124554002	SO:0001819	synonymous_variant	0			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1251G>A	3.37:g.123071312C>T		Somatic	257	0.39	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	124554002	52	43.16	41	B7Z8A6|Q7RTV7|Q8NFM3	Silent	SNP	HMMPfam_Guanylate_cyc,HMMSmart_CYCc,superfamily_A/G_cyclase,HMMPfam_DUF1053,PatternScan_GUANYLATE_CYCLASE_1	p.A417	ENST00000462833.1	37	c.1251	CCDS3022.1	3																																																																																			-	NULL		0.617	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADCY5	protein_coding	OTTHUMT00000355889.4	C	XM_171048		124554002	-1	no_errors	NM_183357.1	genbank	human	validated	54_36p	silent	SNP	0.445	T
EYA4	2070	genome.wustl.edu	37	6	133789862	133789862	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr6:133789862C>A	ENST00000367895.5	+	11	1427	c.963C>A	c.(961-963)aaC>aaA	p.N321K	EYA4_ENST00000525849.1_Missense_Mutation_p.N298K|EYA4_ENST00000452339.2_Missense_Mutation_p.N267K|EYA4_ENST00000355167.3_Missense_Mutation_p.N321K|EYA4_ENST00000431403.2_Missense_Mutation_p.N321K|EYA4_ENST00000355286.6_Missense_Mutation_p.N298K|EYA4_ENST00000430974.2_Missense_Mutation_p.N267K|EYA4_ENST00000531901.1_Missense_Mutation_p.N321K	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	321					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		GACTGACTAACCAACCAGGTA	0.428																																					Melanoma(57;398 1237 3528 4702 7415)	dbGAP											0			6											127.0	119.0	122.0					6																	133789862		2203	4298	6501	133831555	SO:0001583	missense	0			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3522	protein-coding gene	gene with protein product		603550	"""eyes absent (Drosophila) homolog 4"", ""eyes absent homolog 4 (Drosophila)"""	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.963C>A	6.37:g.133789862C>A	ENSP00000356870:p.Asn321Lys	Somatic	235	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	133831555	117	46.15	102	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	HMMPfam_Hydrolase	p.N321K	ENST00000367895.5	37	c.963	CCDS5165.1	6	.	.	.	.	.	.	.	.	.	.	C	14.00	2.403392	0.42613	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	T;T;T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.41	1.71	0.24356	.	2.456060	0.01047	N	0.004412	T	0.55862	0.1947	L	0.29908	0.895	0.30041	N	0.812628	B;B;B;B;B;B	0.17038	0.002;0.009;0.02;0.0;0.009;0.002	B;B;B;B;B;B	0.22152	0.023;0.038;0.014;0.0;0.038;0.023	T	0.36841	-0.9731	10	0.54805	T	0.06	-0.4818	7.0167	0.24892	0.0:0.5043:0.0:0.4957	.	321;267;267;298;321;321	F2Z2Y1;E7ESD5;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;.;EYA4_HUMAN	K	267;267;321;321;298;321;298;321	ENSP00000395916:N267K;ENSP00000388670:N267K;ENSP00000356870:N321K;ENSP00000347294:N321K;ENSP00000347434:N298K;ENSP00000432770:N321K;ENSP00000433219:N298K;ENSP00000404558:N321K	ENSP00000347294:N321K	N	+	3	2	EYA4	133831555	1.000000	0.71417	0.987000	0.45799	0.997000	0.91878	1.126000	0.31344	0.570000	0.29347	0.655000	0.94253	AAC	-	NULL		0.428	EYA4-001	KNOWN	basic|CCDS	protein_coding	EYA4	protein_coding	OTTHUMT00000042282.2	C	NM_004100		133831555	+1	no_errors	NM_004100.4	genbank	human	reviewed	54_36p	missense	SNP	0.993	A
HECW1	23072	genome.wustl.edu	37	7	43547679	43547679	+	Missense_Mutation	SNP	G	G	A	rs367661051		TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr7:43547679G>A	ENST00000395891.2	+	23	4420	c.3815G>A	c.(3814-3816)cGg>cAg	p.R1272Q	AC011738.4_ENST00000436105.1_RNA|HECW1_ENST00000453890.1_Missense_Mutation_p.R1238Q	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1272	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R1251Q(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GCCTATTCGCGGAAAGAGCTC	0.542																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)	7											80.0	82.0	81.0					7																	43547679		1962	4152	6114	43514204	SO:0001583	missense	0			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3815G>A	7.37:g.43547679G>A	ENSP00000379228:p.Arg1272Gln	Somatic	303	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	43514204	115	41.50	83	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_C2,HMMPfam_HECT,HMMSmart_HECTc,superfamily_HECT,HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,superfamily_C2_CaLB	p.R1272Q	ENST00000395891.2	37	c.3815	CCDS5469.2	7	.	.	.	.	.	.	.	.	.	.	G	36	5.933450	0.97116	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.42131	0.98;0.98	5.85	5.85	0.93711	HECT (3);	0.000000	0.85682	D	0.000000	T	0.64068	0.2565	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.892	T	0.63646	-0.6590	10	0.72032	D	0.01	.	20.1669	0.98153	0.0:0.0:1.0:0.0	.	1238;1272	B4DH42;Q76N89	.;HECW1_HUMAN	Q	1272;1238;1272	ENSP00000379228:R1272Q;ENSP00000407774:R1238Q	ENSP00000265522:R1272Q	R	+	2	0	HECW1	43514204	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.779000	0.99018	2.770000	0.95276	0.650000	0.86243	CGG	-	HMMSmart_HECTc,superfamily_HECT		0.542	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HECW1	protein_coding	OTTHUMT00000250893.2	G	NM_015052		43514204	+1	no_errors	NM_015052.3	genbank	human	validated	54_36p	missense	SNP	1.000	A
HSD17B7P2	158160	genome.wustl.edu	37	10	38645312	38645312	+	RNA	SNP	C	C	T			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr10:38645312C>T	ENST00000494540.1	+	0	5					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		GGTGAGGCGGCCCGAAATCGT	0.597																																						dbGAP											0			10																																								38685318			0					10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38645312C>T		Somatic	775	4.67	38		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	38685318	95	36.84	56		RNA	SNP	-	NULL	ENST00000494540.1	37	NULL		10																																																																																			-	-		0.597	HSD17B7P2-001	KNOWN	basic	processed_transcript	HSD17B7P2	pseudogene	OTTHUMT00000047631.2	C	NR_003086		38685318	+1	pseudogene	NR_003086.1	genbank	human	provisional	54_36p	rna	SNP	0.033	T
TCERG1L	256536	genome.wustl.edu	37	10	132891487	132891487	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr10:132891487A>G	ENST00000368642.4	-	12	1784	c.1699T>C	c.(1699-1701)Ttc>Ctc	p.F567L	RP11-462G8.3_ENST00000436942.1_RNA	NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	567	FF 2.									cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		ATAAGTATGAATTGGTTGAAA	0.428																																						dbGAP											0			10											105.0	106.0	106.0					10																	132891487		2203	4300	6503	132781477	SO:0001583	missense	0			AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.1699T>C	10.37:g.132891487A>G	ENSP00000357631:p.Phe567Leu	Somatic	255	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	132781477	132	39.27	86	Q5VWI2|Q86XM8	Missense_Mutation	SNP	HMMPfam_WW,HMMSmart_WW,PatternScan_WW_DOMAIN_1,superfamily_WW_Rsp5_WWP,HMMPfam_FF,HMMSmart_FF,superfamily_FF	p.F567L	ENST00000368642.4	37	c.1699	CCDS7662.2	10	.	.	.	.	.	.	.	.	.	.	A	28.3	4.908969	0.92107	.	.	ENSG00000176769	ENST00000368642	T	0.35421	1.31	4.82	4.82	0.62117	FF domain (4);	0.000000	0.53938	D	0.000051	T	0.37019	0.0988	M	0.71206	2.165	0.80722	D	1	P	0.34864	0.473	B	0.28638	0.092	T	0.40831	-0.9542	10	0.72032	D	0.01	-2.1305	13.573	0.61858	1.0:0.0:0.0:0.0	.	567	Q5VWI1	TCRGL_HUMAN	L	567	ENSP00000357631:F567L	ENSP00000357631:F567L	F	-	1	0	TCERG1L	132781477	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.501000	0.81600	1.801000	0.52704	0.460000	0.39030	TTC	-	HMMPfam_FF,HMMSmart_FF,superfamily_FF		0.428	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TCERG1L	protein_coding	OTTHUMT00000091619.2	A	NM_174937		132781477	-1	no_errors	NM_174937.3	genbank	human	validated	54_36p	missense	SNP	1.000	G
FAM214A	56204	genome.wustl.edu	37	15	52885895	52885895	+	Silent	SNP	A	A	G			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr15:52885895A>G	ENST00000261844.7	-	10	2840	c.2688T>C	c.(2686-2688)atT>atC	p.I896I	RP11-23N2.4_ENST00000562062.1_RNA|FAM214A_ENST00000546305.2_Silent_p.I903I	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	896																	AACCATCAACAATGCCGAGAG	0.383																																						dbGAP											0			15											39.0	33.0	35.0					15																	52885895		1844	4074	5918	50673187	SO:0001819	synonymous_variant	0			AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2688T>C	15.37:g.52885895A>G		Somatic	113	0.00	0		14	41.67	10	WXS	Illumina HiSeq	Phase_IV	50673187	89	31.62	43	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	NULL	p.I896	ENST00000261844.7	37	c.2688	CCDS45263.1	15																																																																																			-	NULL		0.383	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1370	protein_coding	OTTHUMT00000419914.1	A	NM_019600		50673187	-1	no_errors	NM_019600.2	genbank	human	validated	54_36p	silent	SNP	0.992	G
AKAP13	11214	genome.wustl.edu	37	15	86118413	86118413	+	Silent	SNP	G	G	A	rs374214307		TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr15:86118413G>A	ENST00000394518.2	+	6	809	c.714G>A	c.(712-714)ccG>ccA	p.P238P	AKAP13_ENST00000361243.2_Silent_p.P238P	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	238					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						ATGAAATACCGTATGGAGACT	0.448																																					Melanoma(94;603 1453 3280 32295 32951)	dbGAP											0			15						G	,	2,4402	4.2+/-10.8	0,2,2200	143.0	137.0	139.0		714,714	-7.6	0.0	15		139	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	0,2,6499	AA,AG,GG		0.0,0.0454,0.0154	,	238/2818,238/2814	86118413	2,13000	2202	4299	6501	83919417	SO:0001819	synonymous_variant	0			M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.714G>A	15.37:g.86118413G>A		Somatic	202	0.00	0		4	33.33	2	WXS	Illumina HiSeq	Phase_IV	83919417	145	37.55	89	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	HMMPfam_RhoGEF,HMMSmart_RhoGEF,superfamily_DH-domain,HMMPfam_PH,HMMSmart_PH,superfamily_ANK,HMMPfam_C1_1,HMMSmart_C1,PatternScan_ZF_DAG_PE_1,PatternScan_EF_HAND_1,HMMPfam_RII_binding_1,superfamily_SSF50729,superfamily_SSF57889	p.P238	ENST00000394518.2	37	c.714	CCDS32319.1	15																																																																																			-	NULL		0.448	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	AKAP13	protein_coding	OTTHUMT00000417318.1	G	NM_007200		83919417	+1	no_errors	NM_006738.4	genbank	human	reviewed	54_36p	silent	SNP	0.233	A
C17orf97	400566	genome.wustl.edu	37	17	263592	263592	+	Missense_Mutation	SNP	G	G	A	rs71369083|rs71145728|rs532458474|rs71369084		TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr17:263592G>A	ENST00000360127.6	+	2	974	c.958G>A	c.(958-960)Gag>Aag	p.E320K	AC108004.3_ENST00000466740.2_RNA|C17orf97_ENST00000571106.1_Intron	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	350	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CACTGACCCCGAGGCCCTCAA	0.692																																						dbGAP											0			17											20.0	24.0	23.0					17																	263592		2197	4297	6494	263938	SO:0001583	missense	0			AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.958G>A	17.37:g.263592G>A	ENSP00000353245:p.Glu320Lys	Somatic	32	3.03	1		6	0.00	0	WXS	Illumina HiSeq	Phase_IV	263938	19	26.92	7	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	NULL	p.E330K	ENST00000360127.6	37	c.988	CCDS32519.2	17	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608547	0.00842	.	.	ENSG00000187624	ENST00000360127	T	0.31247	1.5	2.05	-4.1	0.03940	.	.	.	.	.	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	9	0.09843	T	0.71	.	1.1097	0.01701	0.4009:0.1978:0.2653:0.136	.	320	Q6ZQX7-4	.	K	320	ENSP00000353245:E320K	ENSP00000353245:E320K	E	+	1	0	C17orf97	263938	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.949000	0.03893	-2.563000	0.00472	-0.974000	0.02594	GAG	-	NULL		0.692	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	C17orf97	protein_coding	OTTHUMT00000255648.4	G	NM_001013672		263938	+1	no_errors	NM_001013672.3	genbank	human	validated	54_36p	missense	SNP	0.000	A
CSH2	1443	genome.wustl.edu	37	17	61950048	61950048	+	Silent	SNP	G	G	A			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr17:61950048G>A	ENST00000392886.2	-	4	496	c.345C>T	c.(343-345)ccC>ccT	p.P115P	CSH2_ENST00000336844.5_Silent_p.P115P|CSH2_ENST00000345366.7_Intron|CSH2_ENST00000560142.1_Silent_p.P58P	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	115						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|lung(3)	6						GGAACCGCACGGGCTCCAGCC	0.592																																						dbGAP											0			17											8.0	9.0	9.0					17																	61950048		2152	4196	6348	59303780	SO:0001819	synonymous_variant	0			V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"""placental lactogen"", ""chorionic somatomammotropin B"""	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.345C>T	17.37:g.61950048G>A		Somatic	99	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	59303780	50	18.03	11	P01243|Q0VDB1|Q14407	Silent	SNP	HMMPfam_Hormone_1,superfamily_4-helical cytokines,PatternScan_SOMATOTROPIN_1,PatternScan_SOMATOTROPIN_2	p.P115	ENST00000392886.2	37	c.345	CCDS42369.1	17																																																																																			-	HMMPfam_Hormone_1,superfamily_4-helical cytokines		0.592	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CSH2	protein_coding	OTTHUMT00000417657.1	G	NM_020991		59303780	-1	no_errors	NM_020991.3	genbank	human	reviewed	54_36p	silent	SNP	0.987	A
NCCRP1	342897	genome.wustl.edu	37	19	39691373	39691373	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr19:39691373G>A	ENST00000339852.4	+	6	827	c.805G>A	c.(805-807)Gtg>Atg	p.V269M		NM_001001414.1	NP_001001414.1	Q6ZVX7	FBX50_HUMAN	non-specific cytotoxic cell receptor protein 1 homolog (zebrafish)	269	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	10						CGACTCCTCCGTGTCTGTGCA	0.622																																					Melanoma(107;1207 1556 14956 29427 52130)	dbGAP											0			19											138.0	137.0	137.0					19																	39691373		2203	4300	6503	44383213	SO:0001583	missense	0			AK123941, BC067874	CCDS12529.1	19q13.2	2013-07-31	2008-11-19		ENSG00000188505	ENSG00000188505			33739	protein-coding gene	gene with protein product		615901					Standard	NM_001001414		Approved	LOC342897, NCCRP-1, FBXO50	uc002okq.1	Q6ZVX7		ENST00000339852.4:c.805G>A	19.37:g.39691373G>A	ENSP00000342137:p.Val269Met	Somatic	86	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	44383213	48	38.46	30	Q6NVV5	Missense_Mutation	SNP	HMMPfam_FBA,superfamily_Gal_bind_like	p.V269M	ENST00000339852.4	37	c.805	CCDS12529.1	19	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094920	0.56075	.	.	ENSG00000188505	ENST00000339852	T	0.54279	0.58	4.96	4.96	0.65561	Galactose-binding domain-like (1);F-box associated (FBA) domain (2);	0.065878	0.64402	D	0.000012	T	0.72859	0.3513	M	0.84683	2.71	0.44677	D	0.997661	D	0.89917	1.0	D	0.75484	0.986	T	0.77148	-0.2694	10	0.87932	D	0	-24.3437	10.8875	0.46976	0.0:0.0:0.812:0.188	.	269	Q6ZVX7	NCRP1_HUMAN	M	269	ENSP00000342137:V269M	ENSP00000342137:V269M	V	+	1	0	NCCRP1	44383213	1.000000	0.71417	0.998000	0.56505	0.359000	0.29487	5.132000	0.64758	2.319000	0.78375	0.484000	0.47621	GTG	-	HMMPfam_FBA,superfamily_Gal_bind_like		0.622	NCCRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCCRP1	protein_coding	OTTHUMT00000463829.1	G	NM_001001414		44383213	+1	no_errors	NM_001001414.1	genbank	human	provisional	54_36p	missense	SNP	1.000	A
ARFGEF2	10564	genome.wustl.edu	37	20	47589698	47589698	+	Silent	SNP	G	G	A			TCGA-AB-2862-03B-01W-0728-08	TCGA-AB-2862-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	2907d873-3189-4bbb-9c40-127d61225086	a8d14ea2-aa95-48c9-8c69-86b8ac62489a	g.chr20:47589698G>A	ENST00000371917.4	+	12	1542	c.1542G>A	c.(1540-1542)gtG>gtA	p.V514V		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	514	HUS; DCB:HUS domain interaction.				endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGTGTGTTGTGGATATTTATG	0.348																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)	dbGAP											0			20											111.0	104.0	107.0					20																	47589698		2203	4300	6503	47023105	SO:0001819	synonymous_variant	0			AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1542G>A	20.37:g.47589698G>A		Somatic	134	0.00	0		11	0.00	0	WXS	Illumina HiSeq	Phase_IV	47023105	104	39.43	69	Q5TFT9|Q9NTS1	Silent	SNP	HMMPfam_Sec7,HMMSmart_Sec7,superfamily_Sec7,HMMPfam_DUF1981,superfamily_ARM-type_fold	p.V514	ENST00000371917.4	37	c.1542	CCDS13411.1	20																																																																																			-	superfamily_ARM-type_fold		0.348	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARFGEF2	protein_coding	OTTHUMT00000079627.1	G	NM_006420		47023105	+1	no_errors	NM_006420.2	genbank	human	reviewed	54_36p	silent	SNP	1.000	A
