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	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
HIVEP3	59269	broad.mit.edu	37	1	42050343	42050343	+	Silent	SNP	T	A	A	rs147545420	byFrequency	TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr1:42050343T>A	uc001cgz.3	-	4	1339	c.126A>T	c.(124-126)ACA>ACT	p.T42T	HIVEP3_uc001cha.3_Silent_p.T42T|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	42					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GGGTGGCAGCTGTGCCGCTGC	0.627													7	186	---	---	---	---	0	0	0.029380	0	0
EFCAB7	84455	broad.mit.edu	37	1	63991290	63991290	+	Nonsense_Mutation	SNP	C	A	A			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr1:63991290C>A	uc001dbf.2	+	2	341	c.47C>A	c.(46-48)TCA>TAA	p.S16*	ITGB3BP_uc001dba.1_5'Flank|ITGB3BP_uc001dbb.1_5'Flank|ITGB3BP_uc001dbc.1_5'Flank|ITGB3BP_uc001dbd.1_5'Flank|ITGB3BP_uc009wak.1_5'Flank	NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	16							calcium ion binding				0						AGTCAGAAATCAACACCTTCA	0.363													10	89	---	---	---	---	4.68919e-08	6.09595e-08	0.069234	1	0
IFFO1	25900	broad.mit.edu	37	12	6664490	6664490	+	Missense_Mutation	SNP	G	T	T			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr12:6664490G>T	uc001qpd.1	-	1	740	c.706C>A	c.(706-708)CCC>ACC	p.P236T	IFFO1_uc001qpe.1_RNA|IFFO1_uc010sfe.1_Missense_Mutation_p.P236T|IFFO1_uc001qpf.1_Missense_Mutation_p.P236T|IFFO1_uc001qpc.1_Missense_Mutation_p.P236T	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2	236						intermediate filament					0						CGGATCTCGGGCGTGATGGTG	0.662													6	116	---	---	---	---	2.0095e-06	2.48795e-06	0.029380	1	0
FLOT2	2319	broad.mit.edu	37	17	27208390	27208390	+	Silent	SNP	C	T	T			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr17:27208390C>T	uc002hdc.2	-	9	1041	c.918G>A	c.(916-918)GTG>GTA	p.V306V		NM_004475	NP_004466	Q14254	FLOT2_HUMAN	flotillin 2	306					cell adhesion|epidermis development	cell surface|endocytic vesicle|endosome|membrane fraction					0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			GGACCTGCTTCACCCTGGGGG	0.627													8	79	---	---	---	---	0	0	0.047766	0	0
ARFGEF2	10564	broad.mit.edu	37	20	47626931	47626931	+	Missense_Mutation	SNP	C	G	G			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr20:47626931C>G	uc002xtx.3	+	27	3899	c.3747C>G	c.(3745-3747)TGC>TGG	p.C1249W	ARFGEF2_uc010zyf.1_Missense_Mutation_p.C542W	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1249					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGACCACTTGCCACATTGTCA	0.507													26	45	---	---	---	---	0	0	0.125774	0	0
OSTC	58505	broad.mit.edu	37	4	109578625	109578625	+	Missense_Mutation	SNP	A	G	G			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr4:109578625A>G	uc003hzb.1	+	3	324	c.253A>G	c.(253-255)ATG>GTG	p.M85V		NM_021227	NP_067050	Q9NRP0	OSTC_HUMAN	DC2 protein	85	Helical; (Potential).					integral to membrane|oligosaccharyltransferase complex				breast(1)	1						ACAATATATTATGGAAGGACT	0.338													6	57	---	---	---	---	0	0	0.021553	0	0
PRSS12	8492	broad.mit.edu	37	4	119256646	119256646	+	Missense_Mutation	SNP	T	C	C			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr4:119256646T>C	uc003ica.1	-	3	849	c.802A>G	c.(802-804)ACG>GCG	p.T268A		NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor	268	SRCR 1.					membrane	scavenger receptor activity			skin(1)	1						AAGCTACACGTGACAGCAGCT	0.398													3	61	---	---	---	---	0	0	0.115264	0	0
SNAP91	9892	broad.mit.edu	37	6	84417639	84417639	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr6:84417639C>T	uc011dze.1	-	2	325	c.8G>A	c.(7-9)GGC>GAC	p.G3D	SNAP91_uc003pkb.2_5'UTR|SNAP91_uc003pkc.2_Missense_Mutation_p.G3D|SNAP91_uc003pkd.2_Missense_Mutation_p.G3D|SNAP91_uc003pka.2_Missense_Mutation_p.G3D|SNAP91_uc011dzf.1_5'UTR	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog	3					clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		GAGCGTTTGGCCCGACATCTT	0.587													3	46	---	---	---	---	0	0	0.115264	0	0
AHR	196	broad.mit.edu	37	7	17370506	17370506	+	Missense_Mutation	SNP	T	A	A			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr7:17370506T>A	uc011jxz.1	+	6	1314	c.701T>A	c.(700-702)TTT>TAT	p.F234Y	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	234					apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					TCATCTGGTTTTCTGGTAAGG	0.274													13	17	---	---	---	---	0	0	0.105934	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				23	32	---	---	---	---	0	0	0.099896	0	0
FAM47A	158724	broad.mit.edu	37	X	34148211	34148211	+	Missense_Mutation	SNP	C	T	T			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chrX:34148211C>T	uc004ddg.2	-	1	2218	c.2185G>A	c.(2185-2187)GTT>ATT	p.V729I		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	729										ovary(4)|central_nervous_system(1)	5						TCGTCAAGAACGTCAGGTTCA	0.438													10	171	---	---	---	---	0	0	0.058154	0	0
Unknown	0	broad.mit.edu	37	16	15457565	15457566	+	IGR	DEL	AC	-	-			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr16:15457565_15457566delAC								PDXDC1 (224370 upstream) : MPV17L (32045 downstream)																							GAGTGAGCAGACACACTCGGGA	0.446													7	52	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	95528084	95528084	+	IGR	DEL	T	-	-	rs11332663		TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr2:95528084delT								ANKRD20B (5264 upstream) : TEKT4 (9148 downstream)																							GTGGGTACTGTTAAGATTTAA	0.552													3	3	---	---	---	---					
RNF160	26046	broad.mit.edu	37	21	30339206	30339206	+	Frame_Shift_Del	DEL	T	-	-			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr21:30339206delT	uc002ymr.2	-	10	1758	c.1745delA	c.(1744-1746)AATfs	p.N582fs	RNF160_uc010gll.1_RNA	NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	536							ligase activity|zinc ion binding				0						AACCTTACCATTTTTTTTTTT	0.378													8	61	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	37822924	37822924	+	IGR	DEL	A	-	-			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr4:37822924delA								RELL1 (134925 upstream) : PGM2 (5358 downstream)																							aaaaaaaaagaaaaaaaaAAA	0.204													4	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	99877753	99877753	+	IGR	DEL	A	-	-	rs33952764		TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr4:99877753delA								EIF4E (25967 upstream) : METAP1 (39035 downstream)																							actctgtctcaaaaaaaaaaa	0.169													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	89498121	89498122	+	IGR	INS	-	A	A			TCGA-ET-A39K-01A-11D-A19J-08	TCGA-ET-A39K-10A-01D-A19M-08									Somatic	Phase_I	Capture				Illumina GAIIx	0ea309c8-f103-4eec-a8bb-329c17387599	2b6cc855-e787-426f-9121-ddbcad17e997	g.chr8:89498121_89498122insA								MMP16 (158404 upstream) : None (None downstream)																							gaacagctatgaaaaaaaaaac	0.158													3	5	---	---	---	---					
