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	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
PEX14	5195	hgsc.bcm.edu	hg19	1	10678475	10678475	+	Splice_Site	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	PEX14	NM_004565	exon5	c.384+1G>A	.	TACAAGGTGAGTC	.	36.0	16.0	50.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
ZCCHC11	23318	hgsc.bcm.edu	hg19	1	52961169	52961169	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ZCCHC11	NM_015269	exon6	c.A1196G	p.Y399C	GAGCCATACAACC	.	65.0	28.0	75.0	0.0	.	151	.	.	.	none	.	.	PASS	Atlas-SNP
SRBD1	55133	hgsc.bcm.edu	hg19	2	45616665	45616665	+	Silent	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SRBD1	NM_018079	exon21	c.C2772G	p.G924G	AACTTTGCCTGTA	.	65.0	17.0	71.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF514	84874	hgsc.bcm.edu	hg19	2	95815137	95815137	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ZNF514	NM_032788	exon5	c.T1093G	p.F365V	TGTGAAATCTGTA	.	74.0	33.0	78.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	hg19	2	198266726	198266726	+	Missense_Mutation	SNP	G	G	T	rs78164940	bycluster	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	SF3B1,NS,carcinoma,0,1	SF3B1	NM_012433	exon15	c.C2206A	p.R736S	GTTGGCGGATACC	.	64.0	4.0	59.0	0.0	.	1038	.	.	.	weak	.	.	PASS	Atlas-SNP
UGT1A3	54659	hgsc.bcm.edu	hg19	2	234638329	234638329	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	UGT1A3	NM_019093	exon1	c.A557G	p.Q186R	GCACACAGTGTCC	.	254.0	122.0	234.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
SCLY	51540	hgsc.bcm.edu	hg19	2	238990470	238990470	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SCLY	NM_016510	exon5	c.T629C	p.I210T	CTGGCATTGTCAT	.	50.0	19.0	62.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD28	23243	hgsc.bcm.edu	hg19	3	15751227	15751227	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ANKRD28	NM_015199	exon13	c.A1264G	p.N422D	GAAGGTTTAGGCA	.	15.0	9.0	11.0	0.0	.	121	.	.	.	none	.	.	PASS	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	hg19	3	45780273	45780273	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SACM1L	NM_014016	exon18	c.G1477A	p.D493N	TTCTAGGATTCCA	.	55.0	31.0	47.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
ACPL2	92370	hgsc.bcm.edu	hg19	3	140979087	140979087	+	Missense_Mutation	SNP	C	C	A	rs367551091	alternate_allele	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ACPL2	NM_152282	exon4	c.C70A	p.L24M	CTCAGCCTGCAGT	.	46.0	22.0	47.0	0.0	.	50	.	.	.	alt	.	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	hg19	4	437056	437056	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ZNF721	NM_133474	exon3	c.G1200C	p.M400I	TGTTGAACTATTA	.	56.0	24.0	59.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
SLC26A1	10861	hgsc.bcm.edu	hg19	4	983983	983983	+	Silent	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SLC26A1	NM_022042	exon3	c.A744G	p.T248T	CAGCCATGTGAGG	.	7.0	5.0	9.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	hg19	4	2824664	2824664	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	SH3BP2,NS,carcinoma,0,1	SH3BP2	NM_001145856	exon3	c.C310T	p.P104S	ACAGGGCCCCTGC	.	33.0	14.0	22.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
MFSD10	10227	hgsc.bcm.edu	hg19	4	2934166	2934166	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MFSD10	NM_001120	exon5	c.T605C	p.M202T	GGTGCCATTTCCA	.	64.0	26.0	69.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
COL25A1	84570	hgsc.bcm.edu	hg19	4	109817832	109817832	+	Silent	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	COL25A1	NM_198721	exon15	c.A897G	p.T299T	TTCGCCTGTGTCA	.	86.0	4.0	87.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	hg19	5	101834204	101834204	+	Silent	SNP	C	C	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SLCO6A1	NM_173488	exon1	c.G345T	p.L115L	TATGAGCAGGATG	.	73.0	35.0	73.0	0.0	.	153	.	.	.	none	.	.	PASS	Atlas-SNP
IL9	3578	hgsc.bcm.edu	hg19	5	135228124	135228124	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	IL9	NM_000590	exon5	c.A391G	p.I131V	GGAAAATTTCCAG	.	49.0	23.0	74.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
SLC35A4	113829	hgsc.bcm.edu	hg19	5	139947279	139947279	+	Silent	SNP	T	T	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SLC35A4	NM_080670	exon3	c.T525A	p.A175A	AGCAGCTGCTGCC	.	73.0	35.0	89.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
TREM2	54209	hgsc.bcm.edu	hg19	6	41129014	41129014	+	Silent	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	TREM2	NM_018965	exon2	c.G378A	p.V126V	CACCTCCACCAGG	.	42.0	13.0	45.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
TJAP1	93643	hgsc.bcm.edu	hg19	6	43466779	43466779	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	TJAP1,NS,carcinoma,0,1	TJAP1	NM_080604	exon4	c.G40C	p.A14P	CGTAAGGCACCAC	.	51.0	4.0	51.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
WDR91	29062	hgsc.bcm.edu	hg19	7	134873248	134873248	+	Silent	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	WDR91	NM_014149	exon13	c.G1818A	p.E606E	GTAGACCTCCCCG	.	304.0	64.0	217.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
VCPIP1	80124	hgsc.bcm.edu	hg19	8	67577113	67577113	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	VCPIP1	NM_025054	exon1	c.T2081C	p.L694P	CCAGTAAGAATAA	.	151.0	58.0	158.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
TAF2	6873	hgsc.bcm.edu	hg19	8	120816142	120816142	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	TAF2	NM_003184	exon5	c.C536T	p.S179F	CCACAAGAGAAAA	.	160.0	75.0	226.0	0.0	.	204	.	.	.	none	.	.	PASS	Atlas-SNP
TNFSF15	9966	hgsc.bcm.edu	hg19	9	117552848	117552848	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	TNFSF15	NM_005118	exon4	c.C640T	p.L214F	CTCCGAGGTAGAT	.	91.0	39.0	84.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
PIP5KL1	138429	hgsc.bcm.edu	hg19	9	130684238	130684238	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	PIP5KL1	NM_001135219	exon10	c.G1073A	p.R358Q	TCCAGCCGCTTGC	.	5.0	4.0	12.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
C9orf69	90120	hgsc.bcm.edu	hg19	9	139008421	139008421	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	C9orf69	NM_152833	exon2	c.G326A	p.R109H	ACCAGGCGGAAGT	.	24.0	12.0	28.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM72	643236	hgsc.bcm.edu	hg19	10	45429133	45429133	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	TMEM72	NM_001123376	exon4	c.G258C	p.W86C	CCACTGGCTGGGC	.	53.0	25.0	54.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGA7B	401647	hgsc.bcm.edu	hg19	10	99619286	99619286	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	GOLGA7B,NS,carcinoma,0,1	GOLGA7B	NM_001010917	exon2	c.C84A	p.S28R	CTACAGCGATGGG	.	65.0	3.0	61.0	1.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
PDZD8	118987	hgsc.bcm.edu	hg19	10	119049814	119049814	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	PDZD8,colon,carcinoma,0,1	PDZD8	NM_173791	exon4	c.C1144G	p.R382G	CAAGACGAAGTGT	.	43.0	0.0	59.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	hg19	11	1275533	1275533	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MUC5B	NM_002458	exon34	c.G15429C	p.M5143I	GTCCATGGATATC	.	53.0	21.0	47.0	0.0	.	473	.	.	.	none	.	.	PASS	Atlas-SNP
LGALS12	85329	hgsc.bcm.edu	hg19	11	63273900	63273900	+	Silent	SNP	G	G	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	LGALS12,bladder,carcinoma,+1,1	LGALS12	NM_001142535	exon1	c.G36C	p.T12T	TGGAACGAGGATC	.	86.0	5.0	103.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
CATSPER1	117144	hgsc.bcm.edu	hg19	11	65788966	65788966	+	Splice_Site	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	CATSPER1	NM_053054	exon5	c.1691+1G>A	.	CACTGACCTGAGC	.	29.0	16.0	56.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
CADM1	23705	hgsc.bcm.edu	hg19	11	115080343	115080343	+	Silent	SNP	G	G	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	CADM1,NS,carcinoma,0,6	CADM1	NM_014333	exon8	c.C1029A	p.T343T	GGTGGTGGTTGTT	.	63.0	3.0	64.0	2.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	hg19	11	118771983	118771983	+	Silent	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	BCL9L	NM_182557	exon6	c.G2469A	p.Q823Q	GCTGTTCTGGGCC	.	92.0	38.0	78.0	0.0	.	254	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGEF12	23365	hgsc.bcm.edu	hg19	11	120352127	120352127	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	ARHGEF12,NS,carcinoma,0,1	ARHGEF12	NM_015313	exon39	c.G4396T	p.A1466S	GATGGGGCAATTT	.	83.0	28.0	94.0	0.0	.	133	.	.	.	none	.	.	PASS	Atlas-SNP
LARP4	113251	hgsc.bcm.edu	hg19	12	50847454	50847454	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	LARP4	NM_001170808	exon9	c.T1016C	p.L339P	CACCACTGGTAAG	.	123.0	59.0	126.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
GRASP	160622	hgsc.bcm.edu	hg19	12	52401016	52401016	+	Silent	SNP	C	C	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	GRASP	NM_181711	exon1	c.C213A	p.L71L	CGCGCTCGCCGTG	.	25.0	14.0	22.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	hg19	15	52338881	52338881	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MAPK6	NM_002748	exon2	c.A224G	p.D75G	ACCATGATAACAT	.	119.0	45.0	132.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
RAB11FIP3	9727	hgsc.bcm.edu	hg19	16	568988	568988	+	Silent	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	RAB11FIP3	NM_014700	exon10	c.G1686A	p.T562T	CTGCACGCCCTGT	.	129.0	34.0	130.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	hg19	16	2155892	2155892	+	Silent	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	PKD1,NS,carcinoma,0,1	PKD1	NM_000296	exon20	c.T7837C	p.L2613L	GGGCCAACGAGTA	.	65.0	3.0	51.0	0.0	.	184	.	.	.	none	.	.	PASS	Atlas-SNP
ULK2	9706	hgsc.bcm.edu	hg19	17	19770705	19770705	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ULK2	NM_001142610	exon1	c.A26T	p.Y9F	TTGCTGTACTCGA	.	51.0	29.0	22.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
EVI2A	2123	hgsc.bcm.edu	hg19	17	29645740	29645740	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	EVI2A,NS,carcinoma,0,1	EVI2A	NM_001003927	exon3	c.T361A	p.S121T	CGACAGAAGGTAT	.	196.0	116.0	122.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
HNF1B	6928	hgsc.bcm.edu	hg19	17	36099582	36099582	+	Silent	SNP	T	T	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	HNF1B	NM_001165923	exon2	c.A393G	p.Q131Q	GTTGTGTTGCTGC	.	68.0	42.0	46.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
KRT26	353288	hgsc.bcm.edu	hg19	17	38926071	38926071	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	KRT26	NM_181539	exon5	c.G904T	p.E302X	TCAGCTCATTTCT	.	214.0	68.0	147.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
NARF	26502	hgsc.bcm.edu	hg19	17	80443514	80443514	+	Silent	SNP	C	C	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	NARF	NM_012336	exon10	c.C1113T	p.V371V	GGAGGTCCTCGCC	.	123.0	86.0	85.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	hg19	18	29788204	29788204	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MEP1B	NM_005925	exon9	c.A889T	p.S297C	CCAGAGAGTGATC	.	83.0	36.0	69.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
PQLC1	80148	hgsc.bcm.edu	hg19	18	77679262	77679262	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	PQLC1	NM_025078	exon5	c.T530A	p.L177Q	ACAGCCAGGAAGC	.	50.0	18.0	58.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	hg19	19	1046944	1046944	+	Missense_Mutation	SNP	C	C	G	rs144979723	bycluster;byfrequency;alternate_allele	TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	ABCA7,colon,carcinoma,0,1	ABCA7	NM_019112	exon14	c.C1766G	p.A589G	GCCGCGCGGTGCT	.	10.0	3.0	8.0	1.0	.	174	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9077786	9077786	+	Silent	SNP	G	G	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MUC16	NM_024690	exon3	c.C9660A	p.I3220I	GGACCTGATCTCT	.	157.0	71.0	162.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
RALGAPB	57148	hgsc.bcm.edu	hg19	20	37153507	37153507	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	RALGAPB	NM_020336	exon11	c.C1706A	p.P569H	CTCCTCCTTTGTT	.	247.0	151.0	171.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
SULF2	55959	hgsc.bcm.edu	hg19	20	46291842	46291842	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SULF2	NM_001161841	exon17	c.A2342T	p.Y781F	TCAAAGTACTCTA	.	98.0	51.0	89.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
DDX27	55661	hgsc.bcm.edu	hg19	20	47835928	47835928	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	DDX27	NM_017895	exon1	c.A36C	p.E12D	CTGCGAAAAGTTA	.	49.0	14.0	39.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
CRYAA	1409	hgsc.bcm.edu	hg19	21	44589374	44589374	+	Silent	SNP	C	C	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	CRYAA	NM_000394	exon1	c.C165G	p.T55T	CCGCACCGTGCTG	.	183.0	92.0	174.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
MED15	51586	hgsc.bcm.edu	hg19	22	20920816	20920816	+	Silent	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	PCQAP,colon,carcinoma,0,2	MED15	NM_015889	exon7	c.G753A	p.Q251Q	GCAACAGCAGCAG	.	46.0	5.0	56.0	2.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
UQCR10	29796	hgsc.bcm.edu	hg19	22	30163434	30163434	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	UQCR10	NM_001003684	exon1	c.G47A	p.R16H	TGTTCCGCAGGAC	.	60.0	29.0	58.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
SEC14L3	266629	hgsc.bcm.edu	hg19	22	30866522	30866522	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SEC14L3	NM_174975	exon2	c.T102A	p.D34E	ATAATCATCAGGG	.	63.0	31.0	61.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
SUN2	25777	hgsc.bcm.edu	hg19	22	39138452	39138452	+	Silent	SNP	G	G	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	SUN2	NM_001199579	exon9	c.C985T	p.L329L	GCTCCAGACGTTC	.	43.0	19.0	53.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM27	57393	hgsc.bcm.edu	hg19	X	15682860	15682860	+	Silent	SNP	A	A	G	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	TMEM27	NM_020665	exon1	c.T39C	p.H13H	TTCAGCATGAATG	.	34.0	26.0	34.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
THOC2	57187	hgsc.bcm.edu	hg19	X	122756985	122756985	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	THOC2	NM_001081550	exon29	c.A3653T	p.K1218I	TCCGATTTAGATG	.	67.0	60.0	73.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF263	10127	hgsc.bcm.edu	hg19	16	3339974	3339974	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	ZNF263	NM_005741	exon6	c.1467delC	p.P489fs	.	.	68.0	19.0	53.0	0.0	.	58	.	0.279412	0	none	.	.	PASS	Atlas-INDEL
MTHFD1	4522	hgsc.bcm.edu	hg19	14	64914978	64914979	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	MTHFD1	NM_005956	exon23	c.2221_2222del	p.741_741del	.	.	47.0	16.0	55.0	0.0	.	61	.	0.340426	0	none	.	.	PASS	Atlas-INDEL
PCDH17	27253	hgsc.bcm.edu	hg19	13	58208351	58208351	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	PCDH17	NM_001040429	exon1	c.1670delC	p.S557fs	.	.	93.0	21.0	78.0	0.0	.	304	.	0.225806	0	none	.	.	PASS	Atlas-INDEL
KIDINS220	57498	hgsc.bcm.edu	hg19	2	8872073	8872073	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8311-01A-11D-2396-08	TCGA-A4-8311-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	ed5c8ff4-0d94-443d-9024-efdae20db5f3	ffccfd57-43fd-497f-b78d-a644b37173b2	.	KIDINS220	NM_020738	exon30	c.4094delC	p.S1365fs	.	.	129.0	43.0	141.0	0.0	.	136	.	0.333333	0	none	.	.	PASS	Atlas-INDEL