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	chromosome_name	start	stop	reference	variant	type	gene_name	transcript_name	transcript_species	transcript_source	transcript_version	strand	transcript_status	trv_type	c_position	amino_acid_change	ucsc_cons	domain	all_domains	deletion_substructures	transcript_error	default_gene_name	gene_name_source	 ensembl_gene_id	tier	dbSNP	GMAF	n_ref_count	n_alt_count	normal_vaf	t_ref_count	t_alt_count	tumor_vaf	n_ref_count_val	n_alt_count_val	normal_vaf_val	t_ref_count_val	t_alt_count_val	tumor_vaf_val
HRNR	0	genome.wustl.edu	37	1	152186899	152186899	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	1	152186899	152186899	C	G	SNP	HRNR	ENST00000368801	human	ensembl	74_37	-1	known	missense	c.7206	p.Q2402H	0.868	NULL	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	-	no_errors	HRNR	HGNC	ENSG00000197915	tier1	-	-	110	0	0.00	106	31	22.63	22	0	0.00	29	5	14.71
HRNR	0	genome.wustl.edu	37	1	152187081	152187081	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	1	152187081	152187081	C	G	SNP	HRNR	ENST00000368801	human	ensembl	74_37	-1	known	missense	c.7024	p.G2342R	0.001	NULL	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	-	no_errors	HRNR	HGNC	ENSG00000197915	tier1	-	-	355	0	0.00	411	109	20.96	113	0	0.00	121	21	14.79
HRNR	0	genome.wustl.edu	37	1	152187037	152187037	+	Silent	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	1	152187037	152187037	C	T	SNP	HRNR	ENST00000368801	human	ensembl	74_37	-1	known	silent	c.7068	p.Q2356	0.000	NULL	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	-	no_errors	HRNR	HGNC	ENSG00000197915	tier1	-	-	416	0	0.00	471	135	22.24	102	0	0.00	121	22	15.38
LRIG3	0	genome.wustl.edu	37	12	59281683	59281683	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	12	59281683	59281683	C	G	SNP	LRIG3	ENST00000320743	human	ensembl	74_37	-1	known	missense	c.979	p.D327H	1.000	smart_Leu-rich_rpt_typical-subtyp	pfam_Ig_I-set,pfam_Leu-rich_rpt,pfam_Immunoglobulin,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	-	no_errors	LRIG3	HGNC	ENSG00000139263	tier1	-	-	40	0	0.00	111	10	8.26	70	0	0.00	132	15	10.20
PKD2	0	genome.wustl.edu	37	4	88929174	88929176	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	GAG	GAG	GAG	-	GAG	GAG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	4	88929174	88929176	GAG	-	DEL	PKD2	ENST00000237596	human	ensembl	74_37	+1	known	in_frame_del	c.289_291	p.E100in_frame_del	1.000:1.000:1.000	NULL	pfam_PKD1_2_channel,pfam_Ion_trans_dom,pfscan_EF_hand_dom,prints_PKD_2,prints_PKD_1	-	no_errors	PKD2	HGNC	ENSG00000118762	tier1			32	0	0.00	42	5	10.64	30	0	0.00	12	2	14.29
QDPR	0	genome.wustl.edu	37	4	17510934	17510934	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	4	17510934	17510934	A	G	SNP	QDPR	ENST00000281243	human	ensembl	74_37	-1	known	missense	c.158	p.I53T	0.022	pfam_DH_sc/Rdtase_SDR	pfam_DH_sc/Rdtase_SDR	-	no_errors	QDPR	HGNC	ENSG00000151552	tier1	-	-	56	0	0.00	66	7	9.59	75	0	0.00	78	7	8.24
ZNF251	0	genome.wustl.edu	37	8	145948119	145948119	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	8	145948119	145948119	A	G	SNP	ZNF251	ENST00000292562	human	ensembl	74_37	-1	known	missense	c.926	p.I309T	0.000	smart_Znf_C2H2-like,pfscan_Znf_C2H2	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	-	no_errors	ZNF251	HGNC	ENSG00000198169	tier1	-	-	59	0	0.00	45	6	11.76	150	0	0.00	117	6	4.88
PCLO	0	genome.wustl.edu	37	7	82581481	82581481	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	7	82581481	82581481	C	T	SNP	PCLO	ENST00000333891	human	ensembl	74_37	-1	known	missense	c.8788	p.V2930I	1.000	NULL	pfam_Znf_piccolo,pfam_C2_dom,pfam_PDZ,superfamily_C2_dom,superfamily_PDZ,superfamily_Znf_FYVE_PHD,smart_PDZ,smart_C2_dom,pfscan_C2_dom,pfscan_PDZ	-	no_errors	PCLO	HGNC	ENSG00000186472	tier1	-	-	87	0	0.00	79	7	8.14	99	0	0.00	72	6	7.69
LAMB1	0	genome.wustl.edu	37	7	107577718	107577718	+	Silent	SNP	G	G	A			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	7	107577718	107577718	G	A	SNP	LAMB1	ENST00000222399	human	ensembl	74_37	-1	known	silent	c.3766	p.L1256	1.000	superfamily_t-SRE	pfam_EGF_laminin,pfam_Laminin_N,superfamily_Prefoldin,superfamily_t-SRE,superfamily_P-loop_NTPase,smart_Laminin_N,smart_EGF_laminin,smart_EG-like_dom,pfscan_Laminin_IV,pfscan_EGF_laminin,pfscan_Laminin_N	-	no_errors	LAMB1	HGNC	ENSG00000091136	tier1	-	-	60	0	0.00	72	14	16.28	81	0	0.00	107	6	5.31
BTN2A3P	0	genome.wustl.edu	37	6	26422387	26422388	+	R	INS	-	-	CTTCCTCCTCCT			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	6	26422387	26422388	-	CTTCCTCCTCCT	INS	BTN2A3P	ENST00000465856	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.003:0.002	-	-	-	no_errors	BTN2A3P	HGNC	ENSG00000124549	tier1			14	0	0.00	8	0	0.00	14	0	0.00	8	0	0.00
TCHH	0	genome.wustl.edu	37	1	152084230	152084235	+	In_Frame_Del	DEL	CAACGT	CAACGT	-			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	CAACGT	CAACGT					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	1	152084230	152084235	CAACGT	-	DEL	TCHH	ENST00000368804	human	ensembl	74_37	-1	known	in_frame_del	c.1463_1458	p.RW487in_frame_del	0.000:0.000:0.000:0.000:0.000:0.000	NULL	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	-	no_errors	TCHH	HGNC	ENSG00000159450	tier1			7	0	0.00	3	0	0.00	7	0	0.00	3	0	0.00
TRIO	0	genome.wustl.edu	37	5	14487871	14487871	+	Silent	SNP	C	C	T			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	5	14487871	14487871	C	T	SNP	TRIO	ENST00000344204	human	ensembl	74_37	+1	known	silent	c.7134	p.P2378	0.171	NULL	pfam_DH-domain,pfam_Prot_kinase_dom,pfam_Spectrin_repeat,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ig_I-set,pfam_SH3_domain,superfamily_Kinase-like_dom,superfamily_DH-domain,superfamily_SH3_domain,superfamily_CRAL-TRIO_dom,superfamily_Capsid/spike_ssD_virus,smart_CRAL-TRIO_dom,smart_Spectrin/alpha-actinin,smart_DH-domain,smart_Pleckstrin_homology,smart_SH3_domain,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_CRAL-TRIO_dom,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom,pfscan_DH-domain	-	no_errors	TRIO	HGNC	ENSG00000038382	tier1	-	-	9	0	0.00	8	4	33.33	6	0	0.00	3	0	0.00
ENSG00000173213	0	genome.wustl.edu	37	18	49507	49507	+	Silent	SNP	G	G	C			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	18	49507	49507	G	C	SNP	ENSG00000173213	ENST00000308911	human	ensembl	74_37	-1	known	silent	c.51	p.G17	0.875	pfam_Tubulin_FtsZ_GTPase,superfamily_Tubulin_FtsZ_GTPase,prints_Tubulin	pfam_Tubulin_FtsZ_GTPase,pfam_Tubulin/FtsZ_2-layer-sand-dom,superfamily_Tubulin_FtsZ_GTPase,superfamily_Tub_FtsZ_C,smart_Tubulin_FtsZ_GTPase,smart_Tubulin/FtsZ_2-layer-sand-dom,prints_Beta_tubulin,prints_Tubulin,prints_Epsilon_tubulin,prints_Gamma_tubulin,prints_Delta_tubulin,prints_Alpha_tubulin	-	no_errors	RP11-683L23.1	Clone_based_vega_gene	ENSG00000173213	tier1	-	-	41	0	0.00	44	5	10.20	0	0	0.00	1	0	0.00
MSH3	0	genome.wustl.edu	37	5	79950700	79950717	+	In_Frame_Del	DEL	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC	-			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	5	79950700	79950717	GCAGCGGCTGCAGCGGCC	-	DEL	MSH3	ENST00000265081	human	ensembl	74_37	+1	known	in_frame_del	c.154_171	p.AAAAAA55in_frame_del	0.640:0.607:0.574:0.541:0.508:0.474:0.440:0.406:0.372:0.338:0.304:0.271:0.238:0.205:0.172:0.140:0.107:0.075	NULL	pfam_D_mismatch_repair_MutS_C,pfam_D_mismatch_repair_MutS_core,pfam_D_mmatch_repair_MutS_con_dom,pfam_D_mismatch_repair_MutS-lik_N,pfam_D_mismatch_repair_MutS_clamp,superfamily_D_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_D_mismatch_repair_MutS_N,superfamily_D_mmatch_repair_MutS_con_dom,smart_D_mismatch_repair_MutS_core,smart_D_mismatch_repair_MutS_C	-	no_errors	MSH3	HGNC	ENSG00000113318	tier1			0	0	0.00	0	0	0.00	0	0	0.00	0	0	0.00
OR2AG1	0	genome.wustl.edu	37	11	6806992	6806992	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	11	6806992	6806992	T	C	SNP	OR2AG1	ENST00000307401	human	ensembl	74_37	+1	known	missense	c.724	p.S242P	0.963	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,pfscan_GPCR_Rhodpsn_7TM	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM	-	no_errors	OR2AG1	HGNC	ENSG00000170803	tier1	-	-	82	0	0.00	70	8	10.26	111	0	0.00	63	2	3.08
ADAMTSL4	0	genome.wustl.edu	37	1	150524368	150524368	+	R	DEL	A	A	-			TCGA-DX-AB2S-01A-11D-A38Z-09	TCGA-DX-AB2S-10A-01D-A38Z-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b1fcf2d5-ca57-48a0-9a53-25a98af18d44	204c8358-19d2-4a10-9df1-fa03c655b6c9	1	150524368	150524368	A	-	DEL	ADAMTSL4	ENST00000483335	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000	-	-	-	no_errors	ADAMTSL4	HGNC	ENSG00000143382	tier1			16	0	0.00	63	7	10.00	18	0	0.00	44	2	4.35