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	transcript_name	strand	transcript_status	amino_acid_change	ucsc_cons	normal_depth	normal_vaf	tumor_depth	tumor_vaf	rna_depth	rna_vaf	polyphen	sift	condel	domain
ACAP3	116983	genome.wustl.edu	37	1	1231487	1231487	+	Silent	SNP	C	C	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_030649.2	-1	validated	p.L470	1.000	46	0%	50	12%	-	-	-	-	-	HMMPfam_ArfGap,HMMSmart_SM00105,superfamily_Pyk2-associated protein beta ARF-GAP domain
ARID1A	8289	genome.wustl.edu	37	1	27100207	27100207	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006015.4	+1	reviewed	p.R1335*	0.945	56	0%	46	39.1%	-	-	-	-	-	NULL
FPGT	8790	genome.wustl.edu	37	1	74670281	74670281	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003838.2	+1	reviewed	p.D184N	1.000	104	0%	94	38.3%	-	-	probably_damaging(0.985)	deleterious(0.02)	deleterious(0.815)	HMMPfam_Fucokinase
NBPF14	25832	genome.wustl.edu	37	1	148011763	148011763	+	Silent	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000310701	-1	known	p.R500K	0.181	11	0%	11	36.4%	-	-	-	-	-	NULL
SMC6	79677	genome.wustl.edu	37	2	17876520	17876520	+	Silent	SNP	T	T	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001142286.1	-1	validated	p.E859	1.000	179	0%	232	50.4%	-	-	-	-	-	HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases
ANKRD36	375248	genome.wustl.edu	37	2	97875549	97875549	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000461153	+1	known	p.E933K	0.035	362	0%	595	14.3%	-	-	benign(0.043)	tolerated(0.27)	neutral(0.036)	NULL
ZNF804A	91752	genome.wustl.edu	37	2	185800787	185800787	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_194250.1	+1	provisional	p.A222P	1.000	39	0%	52	25%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
SF3B1	23451	genome.wustl.edu	37	2	198267350	198267350	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_012433.2	-1	reviewed	p.Q669H	1.000	131	0%	144	42.4%	-	-	probably_damaging(1)	deleterious(0.05)	deleterious(0.845)	superfamily_ARM repeat
ADAM23	8745	genome.wustl.edu	37	2	207460838	207460838	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003812.2	+1	reviewed	p.R771W	1.000	93	0%	102	51%	-	-	possibly_damaging(0.884)	tolerated(0.18)	neutral(0.401)	NULL
EPHB1	2047	genome.wustl.edu	37	3	134825394	134825394	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_004441.4	+1	reviewed	p.R304G	1.000	45	0%	56	16.1%	-	-	probably_damaging(0.999)	tolerated(0.11)	deleterious(0.762)	NULL
TNIK	23043	genome.wustl.edu	37	3	170800136	170800136	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015028.2	-1	validated	p.R1073*	1.000	101	0%	95	35.8%	-	-	-	-	-	HMMPfam_CNH,HMMSmart_SM00036
PIK3CA	5290	genome.wustl.edu	37	3	178936095	178936095	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006218.2	+1	reviewed	p.Q546R	1.000	94	0%	89	41.6%	-	-	probably_damaging(0.998)	deleterious(0.05)	deleterious(0.820)	HMMPfam_PI3Ka,HMMSmart_PI3Ka,superfamily_ARM-type_fold
MUC4	4585	genome.wustl.edu	37	3	195509355	195509355	+	Silent	SNP	T	T	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018406.5	-1	reviewed	p.S2904	0.045	181	0%	231	17.3%	-	-	-	-	-	NULL
MFI2	4241	genome.wustl.edu	37	3	196735829	196735829	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_005929.4	-1	reviewed	p.S511	0.377	81	0%	77	35.1%	-	-	-	-	-	HMMPfam_Transferrin,HMMSmart_SM00094,superfamily_Periplasmic binding protein-like II
RNF212	285498	genome.wustl.edu	37	4	1066796	1066796	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001131034.1	-1	validated	p.P254A	0.000	76	0%	75	32%	-	-	unknown(0)	-	-	NULL
SORCS2	57537	genome.wustl.edu	37	4	7698925	7698925	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020777.2	+1	reviewed	p.G531A	1.000	67	0%	59	27.1%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	HMMSmart_SM00602,superfamily_Oligoxyloglucan reducing end-specific cellobiohydrolase
LOC729862	729862	genome.wustl.edu	37	5	28927120	28927120	+	RNA	SNP	C	C	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_040872.2	+1	model	NULL	0.555	57	0%	50	24%	-	-	-	-	-	-
PLK2	10769	genome.wustl.edu	37	5	57750461	57750461	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006622.2	-1	validated	p.L669F	0.997	157	0%	155	27.1%	-	-	probably_damaging(0.999)	tolerated(0.08)	deleterious(0.790)	HMMPfam_POLO_box,superfamily_SSF82615
TNPO1	3842	genome.wustl.edu	37	5	72192969	72192969	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002270.3	+1	reviewed	p.E777Q	1.000	71	0%	73	24.7%	-	-	probably_damaging(0.989)	deleterious(0)	deleterious(0.884)	superfamily_ARM repeat
LRRTM2	26045	genome.wustl.edu	37	5	138208849	138208849	+	Silent	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015564.2	-1	validated	p.L467	1.000	177	0%	155	28.4%	-	-	-	-	-	NULL
PCDHGA2	56113	genome.wustl.edu	37	5	140720411	140720411	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_018915.2	+1	reviewed	p.E625K	0.999	30	0%	36	25%	-	-	probably_damaging(0.996)	deleterious(0)	deleterious(0.906)	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
GRIA1	2890	genome.wustl.edu	37	5	153175040	153175040	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001114183.1	+1	reviewed	p.P759T	1.000	104	0%	87	33.3%	-	-	possibly_damaging(0.681)	deleterious(0.05)	deleterious(0.589)	HMMPfam_Lig_chan,HMMSmart_PBPe,superfamily_SSF53850
CAGE1	285782	genome.wustl.edu	37	6	7373473	7373473	+	Silent	SNP	T	T	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_205864.2	-1	validated	p.R391	0.580	250	0.4%	231	11.3%	-	-	-	-	-	NULL
BMP5	653	genome.wustl.edu	37	6	55638897	55638897	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_021073.2	-1	reviewed	p.R326L	1.000	173	0%	147	40.8%	-	-	probably_damaging(1)	tolerated(0.1)	deleterious(0.786)	NULL
ME1	4199	genome.wustl.edu	37	6	83937058	83937058	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002395.4	-1	reviewed	p.T424S	0.997	104	0%	99	38.4%	-	-	benign(0.261)	tolerated(0.06)	neutral(0.350)	HMMPfam_Malic_M,superfamily_NAD(P)-bd
ZNF292	23036	genome.wustl.edu	37	6	87953295	87953295	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015021.1	+1	validated	p.R282C	1.000	181	0%	137	29.2%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
MICAL1	64780	genome.wustl.edu	37	6	109771700	109771700	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022765.3	-1	validated	p.R332S	0.807	15	0%	10	40%	-	-	benign(0.002)	tolerated(1)	-	superfamily_FAD/NAD(P)-binding domain
LOC340268	340268	genome.wustl.edu	37	7	9766906	9766906	+	RNA	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	XR_041608.1	+1	model	NULL	1.000	49	0%	58	34.5%	-	-	-	-	-	-
SUMF2	25870	genome.wustl.edu	37	7	56136278	56136278	+	Silent	SNP	G	G	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130069.1	+1	reviewed	p.A76	0.183	72	0%	57	40.4%	-	-	-	-	-	HMMPfam_DUF323
LAMB4	22798	genome.wustl.edu	37	7	107698340	107698340	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_007356.2	-1	validated	p.G1106S	0.001	76	0%	88	56.8%	-	-	benign(0.072)	deleterious(0.02)	neutral(0.388)	HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_EGF/Laminin
IRF5	3663	genome.wustl.edu	37	7	128586026	128586026	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001098629.1	+1	reviewed	p.R108Q	1.000	34	0%	45	44.4%	-	-	possibly_damaging(0.435)	tolerated(0.68)	neutral(0.144)	HMMPfam_IRF,HMMSmart_IRF,superfamily_SSF46785
CDH17	1015	genome.wustl.edu	37	8	95188893	95188893	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001144663.1	-1	reviewed	p.D100	0.931	136	0%	199	22.6%	-	-	-	-	-	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like
MYC	4609	genome.wustl.edu	37	8	128752960	128752960	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_002467.4	+1	reviewed	p.H374R	1.000	41	0%	90	70%	-	-	possibly_damaging(0.677)	deleterious(0)	deleterious(0.685)	HMMPfam_HLH,superfamily_HLH helix-loop-helix DNA-binding domain
KCNK9	51305	genome.wustl.edu	37	8	140630721	140630721	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016601.2	-1	reviewed	p.Y302F	1.000	26	0%	49	28.6%	-	-	possibly_damaging(0.851)	tolerated(0.23)	neutral(0.368)	NULL
RECQL4	9401	genome.wustl.edu	37	8	145740586	145740586	+	Silent	SNP	C	C	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000428558	-1	known	p.G477	0.020	38	0%	34	44.1%	-	-	-	-	-	HMMSmart_SM00487,superfamily_P-loop containing nucleoside triphosphate hydrolases
C10orf54	64115	genome.wustl.edu	37	10	73521700	73521700	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_022153.1	-1	validated	p.L56F	0.000	23	0%	39	25.6%	-	-	possibly_damaging(0.583)	tolerated(0.15)	neutral(0.442)	HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
GLRX3	10539	genome.wustl.edu	37	10	131973150	131973150	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006541.3	+1	provisional	p.D282N	1.000	260	0%	204	29.9%	-	-	possibly_damaging(0.919)	tolerated(0.12)	deleterious(0.630)	HMMPfam_Glutaredoxin,superfamily_Thiordxn-like_fd
PAMR1	25891	genome.wustl.edu	37	11	35515710	35515710	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015430.2	-1	validated	p.V62M	1.000	91	0%	117	35.9%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	NULL
OR5M8	219484	genome.wustl.edu	37	11	56258113	56258113	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001005282.1	-1	provisional	p.T245K	0.023	40	0%	31	32.3%	-	-	probably_damaging(0.999)	deleterious(0)	deleterious(0.935)	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
LTBP3	4054	genome.wustl.edu	37	11	65321625	65321625	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001130144.2	-1	reviewed	p.Y186	0.998	20	0%	13	38.5%	-	-	-	-	-	NULL
ATM	472	genome.wustl.edu	37	11	108175401	108175401	+	Splice_Site	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000051.3	+1	reviewed	e36-1	1.000	138	0%	95	28.4%	-	-	-	-	-	-
OR10G8	219869	genome.wustl.edu	37	11	123900503	123900503	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001004464.1	+1	provisional	p.Y58*	1.000	180	0%	172	40.1%	-	-	-	-	-	HMMPfam_7tm_1,superfamily_Family A G protein-coupled receptor-like
CHD4	1108	genome.wustl.edu	37	12	6697009	6697011	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	TTC	TTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001273.2	-1	reviewed	p.K1191in_frame_del	1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	superfamily_P-loop containing nucleoside triphosphate hydrolases
KRAS	3845	genome.wustl.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529	byCluster	TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033360.2	-1	reviewed	p.G12D	1.000	78	0%	98	52%	-	-	possibly_damaging(0.886)	deleterious(0)	deleterious(0.791)	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases
LRIG3	121227	genome.wustl.edu	37	12	59274659	59274659	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_153377.3	-1	provisional	p.T502M	1.000	147	0%	193	24.4%	-	-	probably_damaging(0.994)	tolerated(0.11)	deleterious(0.724)	HMMPfam_I-set,superfamily_Immunoglobulin
RIMBP2	23504	genome.wustl.edu	37	12	130921738	130921738	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_015347.4	-1	validated	p.S568	0.000	14	0%	12	58.3%	-	-	-	-	-	HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III
MYH7	4625	genome.wustl.edu	37	14	23899003	23899003	+	Silent	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000257.2	-1	reviewed	p.A373	0.106	102	0%	86	33.7%	-	-	-	-	-	HMMPfam_Myosin_head,HMMSmart_SM00242,superfamily_P-loop containing nucleoside triphosphate hydrolases
CYFIP1	23191	genome.wustl.edu	37	15	22940829	22940829	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_014608.2	+1	validated	p.R365H	1.000	26	0%	21	28.6%	-	-	probably_damaging(0.997)	deleterious(0.04)	deleterious(0.815)	HMMPfam_FragX_IP
ZNF280D	54816	genome.wustl.edu	37	15	56993092	56993092	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001002844.1	-1	validated	p.S140	0.008	61	0%	73	31.5%	-	-	-	-	-	NULL
SIN3A	25942	genome.wustl.edu	37	15	75694272	75694280	+	In_Frame_Del	DEL	AATTTTCGT	AATTTTCGT	-	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	AATTTTCGT	AATTTTCGT					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001145357.1	-1	reviewed	p.YEN480in_frame_del	1.000:1.000:1.000:1.000:0.986:1.000:1.000:1.000:1.000	-	-	-	-	-	-	-	-	-	HMMPfam_PAH,superfamily_PAH
SEMA4B	10509	genome.wustl.edu	37	15	90767151	90767151	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_020210.3	+1	validated	p.K375	1.000	32	0%	29	41.4%	-	-	-	-	-	HMMPfam_Sema,HMMSmart_SM00630,superfamily_Sema domain
PIEZO1	9780	genome.wustl.edu	37	16	88792792	88792792	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000451779	-1	known	p.V827I	0.966	36	0%	22	63.6%	-	-	benign(0)	tolerated(1)	-	NULL
SLC5A10	125206	genome.wustl.edu	37	17	18862455	18862455	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152351.3	+1	validated	p.A64V	1.000	30	0%	30	40%	-	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_SSF
PIPOX	51268	genome.wustl.edu	37	17	27371920	27371920	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_016518.2	+1	validated	p.R53Q	1.000	112	0%	104	30.8%	-	-	probably_damaging(1)	deleterious(0.01)	deleterious(0.905)	HMMPfam_DAO,superfamily_FAD/NAD(P)-binding domain
KRTAP4-5	85289	genome.wustl.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGA	rs141265645		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_033188.3	-1	reviewed	p.82in_frame_insLPSCC	0.148:0.743	-	-	-	-	-	-	-	-	-	PatternScan_TNFR_NGFR_1,HMMPfam_Keratin_B2
CD7	924	genome.wustl.edu	37	17	80274787	80274787	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006137.6	-1	reviewed	p.S51	0.000	28	0%	29	55.2%	-	-	-	-	-	HMMSmart_SM00406,HMMSmart_SM00409,HMMPfam_V-set,superfamily_Immunoglobulin
COLEC12	81035	genome.wustl.edu	37	18	333075	333075	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_130386.2	-1	validated	p.E629K	1.000	79	0%	60	40%	-	-	possibly_damaging(0.85)	-	-	HMMPfam_Lectin_C,HMMSmart_SM00034,superfamily_C-type lectin-like
ZNF700	90592	genome.wustl.edu	37	19	12060176	12060176	+	Missense_Mutation	SNP	A	A	G	rs189372843	by1000genomes	TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_144566.1	+1	provisional	p.Y446C	0.006	85	0%	63	33.3%	-	-	probably_damaging(1)	tolerated(0.05)	deleterious(0.845)	HMMPfam_zf-C2H2,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers
ENSG00000233422	0	genome.wustl.edu	37	19	14859127	14859128	+	RNA	INS	-	-	TTTTATTTTA	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	-	-					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000430444	+1	known	NULL	0.237:0.246	-	-	-	-	-	-	-	-	-	-
CABP5	56344	genome.wustl.edu	37	19	48543970	48543970	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_019855.3	-1	reviewed	p.R44*	1.000	49	0%	57	36.8%	-	-	-	-	-	HMMSmart_EFh,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_SSF47473
CPT1C	126129	genome.wustl.edu	37	19	50212045	50212045	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152359.1	+1	provisional	p.P505	0.010	25	0%	22	22.7%	-	-	-	-	-	HMMPfam_Carn_acyltransf,superfamily_CoA-dependent acyltransferases
SIRPB1	10326	genome.wustl.edu	37	20	1546900	1546900	+	Silent	SNP	A	A	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006065.3	-1	reviewed	p.A366	0.000	57	0%	45	42.2%	-	-	-	-	-	NULL
C20orf196	149840	genome.wustl.edu	37	20	5753580	5753580	+	Silent	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_152504.2	+1	predicted	p.A23	0.000	58	0%	67	29.9%	-	-	-	-	-	NULL
ACSS1	84532	genome.wustl.edu	37	20	24990007	24990007	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_032501.2	-1	reviewed	p.V597M	0.987	75	0%	76	35.5%	-	-	benign(0.038)	deleterious(0.03)	neutral(0.366)	superfamily_Acetyl-CoA synthetase-like
HLCS	3141	genome.wustl.edu	37	21	38139568	38139568	+	Silent	SNP	C	C	T	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_000411.5	-1	reviewed	p.P490	0.022	54	0%	56	28.6%	-	-	-	-	-	HMMPfam_BPL_LipA_LipB,superfamily_SSF55681
SEC14L4	284904	genome.wustl.edu	37	22	30887722	30887722	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_174977.3	-1	reviewed	p.F307V	1.000	40	0%	38	36.8%	-	-	probably_damaging(1)	deleterious(0)	deleterious(0.945)	superfamily_Supernatant protein factor (SPF) C-terminal domain
PRICKLE3	4007	genome.wustl.edu	37	X	49032263	49032263	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006150.3	-1	reviewed	p.A536V	0.006	59	0%	47	27.7%	-	-	benign(0.03)	tolerated(0.06)	neutral(0.324)	NULL
CYSLTR1	10800	genome.wustl.edu	37	X	77528311	77528311	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_006639.2	-1	reviewed	p.K311N	1.000	54	0%	78	33.3%	-	-	probably_damaging(0.98)	deleterious(0)	deleterious(0.869)	superfamily_Family A G protein-coupled receptor-like
IRS4	8471	genome.wustl.edu	37	X	107978447	107978447	+	Silent	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_003604.2	-1	reviewed	p.R376	0.642	25	0%	24	58.3%	-	-	-	-	-	NULL
GRIA3	2892	genome.wustl.edu	37	X	122528925	122528925	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	ENST00000264357	+1	known	p.R286P	1.000	75	0%	61	41%	-	-	possibly_damaging(0.934)	tolerated(0.06)	deleterious(0.703)	HMMPfam_ANF_receptor,superfamily_Periplasmic binding protein-like I
BRS3	680	genome.wustl.edu	37	X	135570305	135570305	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BG-A2AE-01A-11D-A16D-09	TCGA-BG-A2AE-10A-01D-A16D-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	NM_001727.1	+1	validated	p.Q11R	0.976	73	0%	80	26.3%	-	-	benign(0.039)	tolerated(0.42)	neutral(0.016)	NULL
