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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
SDC3	9672	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	31347253	31347253	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SDC3-227	NM_014654	exon4	c.C1053A	p.P351P	ACCCTTGGGCAGT	.	96	31	85	0	.	15	13	2	0	0
PPIE	10450	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	40211152	40211152	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PPIE-90	NM_006112	exon7	c.G490A	p.V164I	TCTGATGTCGTGC	.	36	20	49	0	.	42	27	15	0	0
CAP1	10487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	40536545	40536545	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CAP1-91	NM_006367	exon12	c.C1238T	p.T413I	ACAAAACAGATGG	.	128	48	126	0	.	188	121	67	0	0
ZFP69	339559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	40961061	40961061	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_198494	exon6	c.G911T	p.C304F	AGGAATGTGGAAG	.	66	22	62	0	.	4	3	1	0	0
NRD1	4898	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	52256297	52256297	+	Nonsense_Mutation	SNP	C	C	A	rs147279713	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NRD1-90	NM_002525	exon31	c.G3280T	p.E1094X	CACACTCCTTCAG	.	58	26	58	0	C|0.999;T|0.000	47	38	9	0	0
AHCYL1	10768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	110561173	110561173	+	Splice_Site	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	AHCYL1-91	NM_006621	exon13	c.1219-1G>A	.	CTTTCAGACCAGC	.	39	16	35	0	.	0	0	0	0	0
SF3B4	10262	broad.mit.edu	37	1	149897857	149897857	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SF3B4-91	NM_005850	exon4	c.C784T	p.P262S	GTGGGGGCATGGC	.	44	4	34	0	.	58	58	0	0	0
HRNR	388697	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	152188167	152188167	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	HRNR-93	NM_001009931	exon3	c.T5938C	p.Y1980H	ACTCATATGGGCC	.	1470	83	1429	1	.	1	1	0	0	0
COPA	1314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	160305059	160305059	+	Silent	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	COPA-92	NM_001098398	exon4	c.T282C	p.D94D	AATATAATCTAAG	.	28	14	35	0	.	34	20	14	0	0
RBM17	84991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	6157469	6157469	+	Missense_Mutation	SNP	T	T	C	rs200401715		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RBM17-90	NM_001145547	exon12	c.T1156C	p.F386L	GCATGTTTCTACA	.	186	84	203	0	T|1.000;C|0.000	32	18	14	0	0
NUDT5	11164	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	12226925	12226925	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NUDT5-92	NM_014142	exon3	c.G94C	p.E32Q	TTTTTTCAAGCTT	.	35	16	26	0	.	32	22	10	0	0
HSPA14	51182	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	14896200	14896200	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	HSPA14-291	NM_016299	exon9	c.T811A	p.S271T	AAACATTCTTTGT	.	91	12	98	0	.	10	9	1	0	0
FAM13C	220965	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	61112192	61112192	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FAM13C-70	NM_198215	exon3	c.G162T	p.L54L	TTCTACCAGAGCC	.	37	13	26	0	.	0	0	0	0	0
CPEB3	22849	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	10	93999658	93999658	+	Silent	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CPEB3-90	NM_014912	exon2	c.T450G	p.T150T	GGAGAAAGTGCCT	.	30	9	38	0	.	2	0	2	0	0
TLL2	7093	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	10	98145849	98145849	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TLL2-93	NM_012465	exon15	c.C1976G	p.S659C	TGAAGGGAGATCC	.	71	14	82	0	.	0	0	0	0	0
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	104139057	104139057	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	GBF1-91	NM_004193	exon34	c.A4508G	p.H1503R	TGATGCACACCCT	.	107	13	128	0	.	38	31	7	0	0
OR5M3	219482	broad.mit.edu	37	11	56237295	56237295	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	OR5M3-70	NM_001004742	exon1	c.C679T	p.R227C	CTGAGCGCATTCG	.	97	4	86	0	.	0	0	0	0	0
PGA3	643834	hgsc.bcm.edu	37	11	60975055	60975055	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PGA3-24	NM_001079807	exon4	c.A424G	p.M142V	GGCAGCATGACAG	.	575	67	598	0	.	0	0	0	0	0
ALDH3B1	221	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	67787234	67787234	+	Silent	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	.	.	.	.	GCTGCTAGAGCAC	.	199	82	216	1	.	47	32	15	0	0
RAB38	23682	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	87908439	87908439	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RAB38-290	NM_022337	exon1	c.C114T	p.Y38Y	GGCCCGGTAGTGC	.	53	20	71	0	.	0	0	0	0	0
NXPE4	54827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	114450961	114450961	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_001077639	exon5	c.G992A	p.S331N	GCCAAACTACAGG	.	134	54	123	0	.	0	0	0	0	0
DSCAML1	57453	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	117308640	117308640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DSCAML1-159	NM_020693	exon25	c.A4583G	p.E1528G	ATGATCTCGCTGA	.	28	12	39	0	.	2	1	1	0	0
ARF3	377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	49334777	49334777	+	Silent	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ARF3-227	NM_001659	exon2	c.A102G	p.L34L	CTTGTATAGGATG	.	295	98	228	0	.	0	0	0	0	0
KCNH3	23416	broad.mit.edu	37	12	49951572	49951572	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KCNH3-90	NM_012284	exon15	c.G3088A	p.A1030T	GGGCCCGCAGAGC	.	84	4	82	1	.	1	1	0	0	0
SYNE2	23224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	64633956	64633956	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SYNE2-164	NM_182914	exon91	c.T16611A	p.H5537Q	GAATCATGTGCTG	.	51	14	29	0	.	0	0	0	0	0
FBLN5	10516	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	92349359	92349359	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FBLN5-134	NM_006329	exon8	c.C801A	p.G267G	GTATGTGCCGGGC	.	93	39	97	0	.	7	6	1	0	0
VPS39	23339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	42462024	42462024	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	VPS39-229	NM_015289	exon12	c.C1131A	p.P377P	GTCTGTGGGCAGC	.	73	33	89	0	.	26	16	10	0	0
AGPHD1	123688	hgsc.bcm.edu;broad.mit.edu	37	15	78807316	78807316	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	AGPHD1-90	NM_001013619	exon3	c.G344A	p.G115D	ATAGTGGCTCTGA	.	21	6	29	0	.	0	0	0	0	0
POLG	5428	hgsc.bcm.edu;broad.mit.edu	37	15	89865055	89865055	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	POLG-228	NM_002693	exon16	c.A2510G	p.Y837C	GCCCCATAGAGGC	.	111	6	112	0	.	22	20	2	0	0
NOL3	8996	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67208730	67208730	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NOL3-227	NM_001276319	exon5	c.G688A	p.E230K	GAACCGGAGCCGG	.	36	5	32	0	.	93	83	10	0	0
CDYL2	124359	hgsc.bcm.edu;broad.mit.edu	37	16	80654830	80654830	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CDYL2-90	NM_152342	exon4	c.C837A	p.I279I	TTTCATGATCTGC	.	32	7	24	0	.	0	0	0	0	0
ADAD2	161931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	84228709	84228709	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ADAD2-68	NM_139174	exon5	c.G858A	p.A286A	CGCAGCGTTGGTG	.	86	21	77	0	.	0	0	0	0	0
GP1BA	2811	hgsc.bcm.edu	37	17	4837204	4837204	+	Silent	SNP	C	C	T	rs201750628		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_000173	exon2	c.C1305T	p.T435T	CCCGACCACCCCA	.	10	5	7	2	.	0	0	0	0	0
C17orf62	79415	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	80405459	80405459	+	Missense_Mutation	SNP	C	C	T	rs142773924		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	C17orf62-90	NM_001193657	exon4	c.G124A	p.G42R	TACCTCCGCTGTA	.	42	11	33	0	A|0.000;C|1.000;T|0.000	0	0	0	0	0
NCLN	56926	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	3192650	3192650	+	Missense_Mutation	SNP	G	G	A	rs200277850		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NCLN-90	NM_020170	exon2	c.G367A	p.V123I	CAGGACGTCGTCC	.	23	11	47	0	G|0.998;A|0.002	0	0	0	0	0
ZNF709	163051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	12576137	12576137	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ZNF709-90	NM_152601	exon4	c.A599C	p.E200A	CCACATTCCTTAC	.	81	30	92	0	.	13	9	0	4	0
PKN1	5585	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	14581037	14581037	+	Missense_Mutation	SNP	G	G	T	rs149980109	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PKN1-1481	NM_213560	exon19	c.G2374T	p.V792L	CCTGAGGTGCTGA	.	65	7	90	0	G|0.999;A|0.000	275	203	72	0	0
NOTCH3	4854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	15303027	15303027	+	Silent	SNP	G	G	T	rs116044239	by1000genomes;alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NOTCH3-855	NM_000435	exon4	c.C423A	p.R141R	GAGGAAGCGTCCA	.	28	10	34	0	G|0.995;A|0.005	3	3	0	0	0
CLIP3	25999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	36515358	36515358	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CLIP3-94	NM_001199570	exon6	c.T858G	p.N286K	CATGAGATTGCCT	.	70	30	122	0	.	0	0	0	0	0
ASAP2	8853	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	9515054	9515054	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ASAP2-90	NM_001135191	exon17	c.T1727C	p.I576T	AAAAAATCCCACT	.	126	51	107	0	.	4	2	2	0	0
TCF23	150921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	27373231	27373231	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TCF23-90	NM_175769	exon2	c.A463T	p.K155X	CCTCTCAAGGTAA	.	260	107	391	0	.	0	0	0	0	0
SPTBN1	6711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	54852000	54852000	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SPTBN1-140	NM_003128	exon11	c.C1242T	p.L414L	TGAGCTCATAAGA	.	58	10	65	0	.	54	43	11	0	0
RGPD3	653489	broad.mit.edu	37	2	107049631	107049631	+	Silent	SNP	C	C	T	rs2912696		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RGPD3-23	NM_001144013	exon16	c.G2316A	p.A772A	TGAATCCGCATTT	.	358	5	339	1	.	9	0	9	0	0
RGPD3	653489	broad.mit.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	T	C	rs2912695		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RGPD3-23	NM_001144013	exon16	c.A2266G	p.N756D	TATAGTTTTCGAG	.	452	4	480	0	T|1.000;|0.000	13	0	13	0	0
RANBP2	5903	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	109380509	109380509	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RANBP2-675	NM_006267	exon20	c.T3514G	p.F1172V	CCTCACTTTGAGC	.	148	58	132	0	.	2	1	1	0	0
ANKRD30BL	554226	broad.mit.edu	37	2	132911181	132911181	+	RNA	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	.	.	.	.	CATGTAGCTTCAG	.	34	12	23	0	.	0	0	0	0	0
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	141816463	141816463	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRP1B-311	NM_018557	exon9	c.C1397G	p.T466S	GGTTGAGTTCTTT	.	31	14	28	0	.	0	0	0	0	0
LRP1B	53353	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	141816476	141816476	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRP1B-311	NM_018557	exon9	c.T1384A	p.Y462N	TTTGATAAATTCG	.	30	10	28	0	.	0	0	0	0	0
PYGB	5834	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	25271238	25271238	+	Missense_Mutation	SNP	G	G	A	rs139162483		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PYGB-91	NM_002862	exon16	c.G1949A	p.R650H	ACTACCGTGTGTC	.	272	161	231	0	G|1.000;A|0.000	225	57	168	0	0
KIF3B	9371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	30897803	30897803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIF3B-517	NM_004798	exon2	c.G223A	p.E75K	TACGATGAGACGT	.	149	84	100	0	.	37	7	30	0	0
MROH8	140699	broad.mit.edu;ucsc.edu	37	20	35800375	35800375	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	.	.	.	.	GGCCTCACTGAGC	.	20	11	13	0	.	4	1	3	0	0
SDC4	6385	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	43959164	43959164	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SDC4-90	NM_002999	exon4	c.G287T	p.G96V	TGGCTCCCAGACC	.	66	17	52	0	.	442	316	125	1	0
ARFGEF2	10564	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	47628619	47628619	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ARFGEF2-358	NM_006420	exon28	c.C3916A	p.R1306R	AGGCCTCGGGTTC	.	109	61	97	0	.	0	0	0	0	0
CDH26	60437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	58569544	58569544	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CDH26-93	NM_177980	exon11	c.G1666C	p.G556R	AATTGGGGTGAGT	.	74	24	62	0	.	0	0	0	0	0
NCAM2	4685	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	22849618	22849618	+	Missense_Mutation	SNP	A	A	G	rs201923816		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NCAM2-94	NM_004540	exon15	c.A1903G	p.K635E	AAAGATAAGGAAG	.	36	12	45	0	A|0.999;G|0.001	0	0	0	0	0
MRPL40	64976	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	19423455	19423455	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MRPL40-90	NM_003776	exon4	c.G591T	p.K197N	CACCAAGGTGTAC	.	63	23	80	0	.	85	56	29	0	0
KLHL22	84861	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	20796432	20796432	+	Silent	SNP	G	G	C	rs149300605	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KLHL22-278	NM_032775	exon7	c.C1833G	p.A611A	CGGGTCGGCCTGG	.	67	26	65	0	G|1.000;A|0.000	14	6	8	0	0
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	46765598	46765598	+	Silent	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CELSR1-525	NM_014246	exon26	c.T7863C	p.A2621A	TATAACAGCTCCG	.	63	24	78	0	.	0	0	0	0	0
MIOX	55586	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	50926723	50926723	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MIOX-90	NM_017584	exon5	c.G360T	p.G120G	CGTCGGGCTCCTG	.	38	16	65	0	.	755	355	399	0	1
HYAL2	8692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	50357591	50357591	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	HYAL2-279	NM_033158	exon3	c.G330A	p.R110R	CATCTTCCGGTGT	.	87	30	105	0	.	36	21	15	0	0
CACNA1D	776	broad.mit.edu	37	3	53808687	53808687	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CACNA1D-100	NM_000720	exon35	c.C4244T	p.A1415V	CCCAGGCGGTGCT	.	103	4	80	0	.	10	10	0	0	0
MITF	4286	ucsc.edu	37	3	69988280	69988280	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MITF-524	NM_198159	exon4	c.C614T	p.A205V	ACAGGGCAGAGAG	.	36	4	38	0	.	17	17	0	0	0
MFN1	55669	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	179076735	179076735	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MFN1-155	NM_033540	exon4	c.A356C	p.D119A	GAACTGATGGAGA	.	81	27	64	0	.	15	10	5	0	0
USP13	8975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	179426711	179426711	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	USP13-659	NM_003940	exon6	c.C771A	p.A257A	ACTAGCCGTGAAA	.	73	33	92	0	.	2	1	1	0	0
CPN2	1370	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	194062198	194062198	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CPN2-73	NM_001080513	exon2	c.C1234A	p.Q412K	TGTACTGCTGCAG	.	76	28	84	0	.	2	1	1	0	0
ODAM	54959	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	71064324	71064324	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ODAM-134	NM_017855	exon5	c.T404A	p.M135K	TCAAAATGCCTCA	.	91	6	73	0	.	0	0	0	0	0
SLC4A4	8671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	72429564	72429564	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SLC4A4-95	NM_001098484	exon24	c.A3154G	p.M1052V	GACATCATGGAAC	.	122	45	112	0	.	29	12	17	0	0
EXOSC9	5393	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	122724130	122724130	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	EXOSC9-90	NM_001034194	exon4	c.G342A	p.K114K	TTCGAAGTGTATA	.	69	32	74	0	.	14	10	4	0	0
BDP1	55814	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	70813231	70813231	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	BDP1-92	NM_018429	exon22	c.T4943A	p.V1648E	GTCAGGTGGTTCT	.	76	32	43	0	.	0	0	0	0	0
VCAN	1462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	82836395	82836395	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	VCAN-238	NM_004385	exon8	c.A7573T	p.R2525W	CGTTTCAGGGAAT	.	56	21	56	0	.	34	22	12	0	0
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140724915	140724915	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PCDHGA3-68	NM_032011	exon1	c.A1315C	p.T439P	CACATCACCCTGC	.	187	32	170	1	.	1	1	0	0	0
PCDHGA3	56112	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140724920	140724920	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PCDHGA3-68	NM_032011	exon1	c.G1320T	p.L440L	CACCCTGCATGTG	.	205	36	176	0	.	0	0	0	0	0
TNIP1	10318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	150444534	150444534	+	Silent	SNP	C	C	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TNIP1-91	NM_001252385	exon2	c.G123C	p.G41G	CTTTATCCCTTGC	.	128	45	151	0	.	0	0	0	0	0
WWC1	23286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	167833322	167833322	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	WWC1-157	NM_015238	exon6	c.A710C	p.D237A	AGCAAGATCTCAT	.	165	70	184	0	.	0	0	0	0	0
DDR1	780	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	30865203	30865203	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DDR1-1403	NM_013994	exon14	c.C2063A	p.P688Q	AGGACCCAAACAT	.	70	25	83	0	.	296	157	138	0	1
KIFC1	3833	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	33365943	33365943	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIFC1-90	NM_002263	exon2	c.G150T	p.K50N	TGAGAAGGTGAGC	.	49	15	60	0	.	0	0	0	0	0
PLEKHG1	57480	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	151117019	151117019	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PLEKHG1-92	NM_001029884	exon6	c.T610G	p.Y204D	ACCCAGTATTGCA	.	114	48	127	0	.	0	0	0	0	0
MLLT4	4301	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	168349109	168349109	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MLLT4-685	NM_001040000	exon28	c.A3761T	p.E1254V	ATGAGGAAAAGCC	.	53	24	55	0	.	8	8	0	0	0
OGDH	4967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	44747234	44747234	+	Silent	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	OGDH-228	NM_002541	exon22	c.T2850C	p.N950N	CCCCAATGCTGAG	.	239	66	186	0	.	114	77	37	0	0
GTF2IRD1	9569	hgsc.bcm.edu;broad.mit.edu	37	7	73932549	73932549	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	GTF2IRD1-94	NM_001199207	exon5	c.G598A	p.G200R	GTGCAGGGGCTGC	.	48	3	37	1	.	6	6	0	0	0
SSPO	23145	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	149502569	149502569	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_198455	exon57	c.C8382A	p.G2794G	AGGGGGCCCTGGC	.	85	16	69	0	.	0	0	0	0	0
UBE3C	9690	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	156963038	156963038	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	UBE3C-704	NM_014671	exon4	c.T236A	p.L79X	CTACCTTGTCACA	.	158	43	97	0	.	30	26	4	0	0
KIF13B	23303	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	28991587	28991587	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIF13B-22	NM_015254	exon22	c.G2754A	p.P918P	GCAGTGCGGCTCC	.	52	19	37	0	.	6	3	3	0	0
SPTLC1	10558	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	94821490	94821490	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SPTLC1-154	NM_006415	exon7	c.C661T	p.L221L	CTTTTAGTAGTCG	.	25	10	20	0	.	37	20	17	0	0
OR1L8	138881	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	125330116	125330116	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	OR1L8-70	NM_001004454	exon1	c.G641A	p.C214Y	GCAATGCAGAGAA	.	48	23	33	0	.	0	0	0	0	0
NXT2	55916	hgsc.bcm.edu;broad.mit.edu	37	X	108780250	108780250	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NXT2-109	NM_018698	exon2	c.G180A	p.L60L	GTCTCTGGTGAGT	.	15	6	20	0	.	0	0	0	0	0
THOC2	57187	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	122755201	122755201	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	THOC2-133	NM_001081550	exon31	c.A4023T	p.K1341N	CTTAAATTTCTCA	.	68	56	74	0	.	15	0	15	0	0
RBMX	27316	hgsc.bcm.edu	37	X	135960073	135960073	+	Splice_Site	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RBMX-131	NM_002139	exon5	c.388+1G>A	.	TTATTACCCATGT	.	50	4	44	1	.	0	0	0	0	0
PRMT6	55170	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	107600260	107600260	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PRMT6-90	NM_018137	exon1	c.923delC	p.S308fs	.	.	83	37	93	0	.	0	0	0	0	0
POLR3C	10623	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	145592731	145592731	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	POLR3C-91	NM_006468	exon15	c.1564delC	p.L522fs	.	.	83	30	96	0	.	0	0	0	0	0
FOXJ2	55810	broad.mit.edu	37	12	8200558	8200560	+	In_Frame_Del	DEL	CAG	CAG	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FOXJ2-230	NM_018416	exon7	c.898_900del	p.300_300del	CCTCAACAGCAGC	.	100	9	51	0	.	0	0	0	0	0
CHD8	57680	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	21870158	21870158	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CHD8-277	NM_001170629	exon19	c.4020delC	p.T1340fs	.	.	141	63	151	0	.	0	0	0	0	0
SMG1	23049	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	18856931	18856931	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SMG1-1160	NM_015092	exon39	c.6039delG	p.L2013fs	.	.	140	84	99	0	.	0	0	0	0	0
LOC100132247	0	broad.mit.edu	37	16	22545580	22545585	+	In_Frame_Del	DEL	AATCTC	AATCTC	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AATCTC	AATCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_001135865	exon7	c.1276_1281del	p.426_427del	GATGATAATCTCA	.	203	6	160	0	.	0	0	0	0	0
PIP5K1C	23396	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	3653310	3653310	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PIP5K1C-267	NM_001195733	exon7	c.899delA	p.K300fs	.	.	67	24	74	0	.	0	0	0	0	0
FBXO36	130888	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	230861514	230861516	+	In_Frame_Del	DEL	AAT	AAT	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FBXO36-227	NM_174899	exon3	c.253_255del	p.85_85del	.	.	115	47	152	0	.	0	0	0	0	0
PARP14	54625	hgsc.bcm.edu	37	3	122433232	122433232	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PARP14-525	NM_017554	exon12	c.3956delA	p.E1319fs	.	.	60	10	44	0	.	0	0	0	0	0
CEP63	80254	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	134267996	134267996	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CEP63-493	NM_025180	exon11	c.1160delA	p.E387fs	.	.	52	16	38	0	.	0	0	0	0	0
SHROOM3	57619	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	77661360	77661360	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SHROOM3-93	NM_020859	exon5	c.2034delG	p.L678fs	.	.	165	83	156	0	.	0	0	0	0	0
GPANK1	7918	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	31632033	31632035	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	GPANK1-91	NM_001199238	exon3	c.221_223del	p.74_75del	.	.	92	34	95	0	.	0	0	0	0	0
TMEM60	85025	broad.mit.edu	37	7	77423460	77423460	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TMEM60-90	NM_032936	exon2	c.231delA	p.K77fs	CCAGGCTTTTTTT	.	199	8	121	0	.	0	0	0	0	0
DDX58	23586	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	9	32467853	32467868	+	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DDX58-230	NM_014314	exon15	c.2077_2092del	p.693_698del	.	.	54	21	78	0	.	0	0	0	0	0
WWC3	55841	broad.mit.edu;bcgsc.ca	37	X	10094307	10094307	+	Nonsense_Mutation	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	WWC3-134	NM_015691	exon15	c.2067delC	p.Y689X	GTTATACGTGTGT	.	75	11	84	0	.	0	0	0	0	0
SCAPER	49855	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	76726602	76726603	+	Frame_Shift_Ins	INS	-	-	TA	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SCAPER-137	NM_020843	exon25	c.3128_3129insTA	p.K1043fs	.	.	95	36	91	0	.	0	0	0	0	0
CHMP2A	27243	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	59063432	59063433	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CHMP2A-90	NM_198426	exon4	c.469_470insA	p.E157fs	.	.	216	80	281	0	.	0	0	0	0	0
NEUROD6	63974	broad.mit.edu	37	7	31378634	31378635	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NEUROD6-92	NM_022728	exon2	c.249_250insA	p.K83fs	TGTTGTCTTTTTT	.	357	0	220	0	.	0	0	0	0	0
LRRC55	219527	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	56949791	56949792	+	Missense_Mutation	DNP	AA	AA	TC	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRRC55		exon1	c.A425C	p.N142S	ACAACAACTCCTT	.	41.0	16.0	50.0	0.0	.	0	0	0	0	0
CUL9	23113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	43153712	43153713	+	Missense_Mutation	DNP	TC	TC	CT	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CUL9		exon4	c.C771T	p.F257S	GCTTTTCTCCTTG	.	71.0	30.0	67.0	0.0	.	0	0	0	0	0