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	dbSNP_AF	Algorithm
ST6GALNAC5	81849	hgsc.bcm.edu	hg19	1	77528719	77528719	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ST6GALNAC5	NM_030965	exon5	c.G839A	p.C280Y	ATGAATGTACAAT	.	142.0	70.0	176.0	0.0	.	59	.	.	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	hg19	1	109814047	109814047	+	Silent	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	CELSR2	NM_001408	exon27	c.G7716A	p.L2572L	GCTGCTGAGCGCC	.	154.0	76.0	179.0	0.0	.	228	.	.	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	hg19	1	118535171	118535171	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	SPAG17	NM_206996	exon36	c.C5279T	p.P1760L	ACACTGGGGCTCT	.	119.0	58.0	151.0	0.0	.	263	.	.	Atlas-SNP
SNTG2	54221	hgsc.bcm.edu	hg19	2	1371215	1371215	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	SNTG2	NM_018968	exon17	c.G1589T	p.S530I	GTCAGAGTCTTGC	.	235.0	53.0	157.0	0.0	.	125	.	.	Atlas-SNP
THADA	63892	hgsc.bcm.edu	hg19	2	43779386	43779386	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	THADA,NS,carcinoma,0,1	THADA	NM_001083953	exon18	c.C2767T	p.R923X	GGACTCGCCCATA	.	319.0	229.0	179.0	0.0	.	131	.	.	Atlas-SNP
CCDC74B	91409	hgsc.bcm.edu	hg19	2	130898811	130898811	+	Silent	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	CCDC74B,NS,carcinoma,0,1	CCDC74B	NM_207310	exon4	c.C603A	p.P201P	CTTCTGGGGGACG	.	158.0	75.0	230.0	1.0	.	27	.	.	Atlas-SNP
ITGB6	3694	hgsc.bcm.edu	hg19	2	161055767	161055767	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ITGB6	NM_000888	exon2	c.G64A	p.G22S	CACAGCCACCTAG	.	474.0	92.0	587.0	1.0	.	68	.	.	Atlas-SNP
AGPS	8540	hgsc.bcm.edu	hg19	2	178301722	178301722	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	AGPS,NS,carcinoma,0,1	AGPS	NM_003659	exon5	c.G577C	p.E193Q	CTTCATGAGATAT	.	44.0	2.0	48.0	0.0	.	56	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179494983	179494983	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	TTN_ENST00000359218,NS,carcinoma,0,5	TTN	NM_001267550	exon239	c.C44266A	p.H14756N	GGAGGTGGGCACT	.	106.0	52.0	137.0	1.0	.	18412	.	.	Atlas-SNP
ARMC9	80210	hgsc.bcm.edu	hg19	2	232087516	232087516	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ARMC9	NM_025139	exon6	c.A580G	p.K194E	ACGCCAAAGCTTT	.	125.0	56.0	131.0	0.0	.	129	.	.	Atlas-SNP
ANO10	55129	hgsc.bcm.edu	hg19	3	43618347	43618347	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	ANO10,NS,carcinoma,0,1	ANO10	NM_018075	exon6	c.G999A	p.M333I	AATCATCATGACA	.	202.0	92.0	288.0	0.0	.	70	.	.	Atlas-SNP
CCDC71	64925	hgsc.bcm.edu	hg19	3	49200783	49200783	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	CCDC71	NM_022903	exon2	c.C859G	p.R287G	GTGTTCGAGCTAC	.	23.0	12.0	34.0	0.0	.	33	.	.	Atlas-SNP
TMEM110-MUSTN1	100526772	hgsc.bcm.edu	hg19	3	52867655	52867655	+	Silent	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	.	NM_001198974	exon9	c.C990A	p.T330T	CTGGTAGGTCTTG	.	99.0	43.0	96.0	0.0	.	.	.	.	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	hg19	3	58107094	58107094	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	FLNB	NM_001457	exon20	c.C2990G	p.T997R	CTGTGACAGGCCG	.	103.0	52.0	153.0	0.0	.	430	.	.	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	hg19	3	73433851	73433851	+	Silent	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	PDZRN3,colon,carcinoma,0,1	PDZRN3	NM_015009	exon10	c.C1866T	p.N622N	AGACTCGTTGCTG	.	55.0	26.0	111.0	1.0	.	196	.	.	Atlas-SNP
EPHA6	285220	hgsc.bcm.edu	hg19	3	97194245	97194245	+	Silent	SNP	C	C	T	rs372907476		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	EPHA6	NM_001080448	exon8	c.C1944T	p.A648A	CACCGCCGCTGTT	.	83.0	14.0	89.0	0.0	.	439	.	.	Atlas-SNP
LRRC33	375387	hgsc.bcm.edu	hg19	3	196386948	196386948	+	Missense_Mutation	SNP	C	C	T	rs368543951		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	LRRC33,caecum,carcinoma,0,1	LRRC33	NM_198565	exon3	c.C434T	p.T145M	CCCTGACGGAGGA	.	43.0	7.0	97.0	1.0	.	91	.	.	Atlas-SNP
WDR1	9948	hgsc.bcm.edu	hg19	4	10077080	10077080	+	Silent	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	WDR1	NM_017491	exon15	c.C1743T	p.S581S	GGCCAGGCTGCTG	.	200.0	68.0	387.0	1.0	.	93	.	.	Atlas-SNP
ARL9	132946	hgsc.bcm.edu	hg19	4	57389953	57389953	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ARL9	NM_206919	exon4	c.A283G	p.T95A	TTTGGAACCTACC	.	91.0	80.0	201.0	0.0	.	10	.	.	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	hg19	5	82835447	82835447	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	VCAN	NM_004385	exon8	c.A6625C	p.T2209P	TTAGCTACTGCAT	.	109.0	58.0	123.0	0.0	.	498	.	.	Atlas-SNP
GFRA3	2676	hgsc.bcm.edu	hg19	5	137593407	137593407	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	GFRA3,colon,carcinoma,0,1	GFRA3	NM_001496	exon4	c.G706A	p.A236T	TGGGGGCGATGGT	.	8.0	5.0	15.0	0.0	.	36	.	.	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	hg19	5	180048543	180048543	+	Silent	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	FLT4	NM_182925	exon13	c.G2019A	p.Q673Q	CTCACCCTGCACC	.	59.0	18.0	164.0	0.0	.	356	.	.	Atlas-SNP
ZFP62	643836	hgsc.bcm.edu	hg19	5	180276821	180276821	+	Silent	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ZFP62	NM_001172638	exon2	c.A1674G	p.E558E	AGGTCGTTCCCCA	.	66.0	19.0	66.0	0.0	.	33	.	.	Atlas-SNP
ZNF76	7629	hgsc.bcm.edu	hg19	6	35262247	35262247	+	Silent	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ZNF76	NM_003427	exon13	c.C1509T	p.T503T	CATTACCTCTGGG	.	104.0	5.0	332.0	0.0	.	37	.	.	Atlas-SNP
THEMIS	387357	hgsc.bcm.edu	hg19	6	128134854	128134854	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	THEMIS	NM_001010923	exon4	c.A932G	p.K311R	TACTTTTTGTGGA	.	59.0	46.0	118.0	0.0	.	168	.	.	Atlas-SNP
SNX13	23161	hgsc.bcm.edu	hg19	7	17890006	17890006	+	Silent	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	SNX13	NM_015132	exon11	c.A1029G	p.V343V	GTCACATACCTTC	.	62.0	27.0	78.0	0.0	.	113	.	.	Atlas-SNP
HDAC9	9734	hgsc.bcm.edu	hg19	7	18869095	18869095	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	HDAC9	NM_178425	exon18	c.T2390A	p.F797Y	TCTGCTTTTTTAA	.	67.0	15.0	70.0	0.0	.	560	.	.	Atlas-SNP
SKAP2	8935	hgsc.bcm.edu	hg19	7	26765154	26765154	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	SKAP2	NM_003930	exon9	c.A689G	p.Y230C	TCATCATAATCCT	.	44.0	24.0	64.0	0.0	.	40	.	.	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	hg19	7	42004352	42004352	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	GLI3	NM_000168	exon15	c.C4319A	p.S1440Y	TGACCAGAGTAAT	.	196.0	88.0	222.0	0.0	.	312	.	.	Atlas-SNP
BPGM	669	hgsc.bcm.edu	hg19	7	134346580	134346580	+	Silent	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	BPGM	NM_199186	exon3	c.T321C	p.H107H	GAATCATGGTGAA	.	294.0	120.0	301.0	1.0	.	12	.	.	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	hg19	8	27255270	27255270	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	PTK2B	NM_173174	exon7	c.A169T	p.K57X	AACTTCAAACTGG	.	236.0	97.0	286.0	0.0	.	304	.	.	Atlas-SNP
TLE1	7088	hgsc.bcm.edu	hg19	9	84208095	84208095	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TLE1	NM_005077	exon15	c.C1426A	p.R476S	TCTGGCGAGCATG	.	136.0	50.0	237.0	0.0	.	81	.	.	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	hg19	9	113173839	113173839	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	SVEP1	NM_153366	exon37	c.A6152G	p.Y2051C	AGGCTGTAACCAT	.	64.0	43.0	80.0	0.0	.	326	.	.	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	hg19	9	130493535	130493535	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TTC16	NM_144965	exon14	c.G2473C	p.G825R	GGCCAGGGCCAGA	.	186.0	51.0	297.0	0.0	.	55	.	.	Atlas-SNP
ZDHHC12	84885	hgsc.bcm.edu	hg19	9	131483968	131483968	+	Silent	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ZDHHC12	NM_032799	exon4	c.G444A	p.L148L	CAGCTGCAGCGCC	.	267.0	31.0	618.0	0.0	.	14	.	.	Atlas-SNP
POLR3A	11128	hgsc.bcm.edu	hg19	10	79769701	79769701	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	POLR3A	NM_007055	exon13	c.C1691A	p.A564D	TGGCAAGCCTTGG	.	78.0	4.0	211.0	0.0	.	104	.	.	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	hg19	10	95111015	95111015	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	MYOF	NM_013451	exon35	c.C3860T	p.A1287V	TTTGGCGCCCTTT	.	71.0	15.0	208.0	0.0	.	177	.	.	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	hg19	11	56468748	56468748	+	Silent	SNP	T	T	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	.	NM_001013358	exon1	c.T885C	p.D295D	TAAGGATGTGAAA	.	36.0	5.0	49.0	0.0	.	.	.	.	Atlas-SNP
ZDHHC5	25921	hgsc.bcm.edu	hg19	11	57466587	57466587	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ZDHHC5	NM_015457	exon11	c.G1679T	p.R560L	CGGGCCGTGAGGA	.	63.0	15.0	92.0	0.0	.	49	.	.	Atlas-SNP
PRCP	5547	hgsc.bcm.edu	hg19	11	82571056	82571056	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	PRCP	NM_199418	exon3	c.G335T	p.G112V	TCATTACCAGTGT	.	125.0	31.0	155.0	0.0	.	69	.	.	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	hg19	12	2229596	2229596	+	Silent	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	CACNA1C	NM_001129831	exon3	c.G477T	p.L159L	CAACCTGGTAAGT	.	101.0	86.0	224.0	1.0	.	1023	.	.	Atlas-SNP
PRICKLE1	144165	hgsc.bcm.edu	hg19	12	42853904	42853904	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	PRICKLE1	NM_001144882	exon8	c.G2203A	p.A735T	CATGGGCGTACTG	.	78.0	27.0	92.0	0.0	.	105	.	.	Atlas-SNP
TAOK3	51347	hgsc.bcm.edu	hg19	12	118588808	118588808	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TAOK3	NM_016281	exon21	c.C2691A	p.Y897X	TCATCTGTAGTCC	.	36.0	6.0	37.0	0.0	.	151	.	.	Atlas-SNP
DCLK1	9201	hgsc.bcm.edu	hg19	13	36700222	36700222	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	DCLK1_ENST00000255448,colon,carcinoma,0,2	DCLK1	NM_004734	exon2	c.C53T	p.A18V	CTCTGCGCCTTAT	.	22.0	21.0	69.0	0.0	.	350	.	.	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	hg19	14	30066720	30066720	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	PRKD1	NM_002742	exon16	c.C2411A	p.P804H	TTCCAGGGATTTG	.	78.0	41.0	87.0	0.0	.	316	.	.	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	hg19	15	31294718	31294718	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TRPM1	NM_001252020	exon27	c.A4236T	p.K1412N	TTCTTCTTTTTTA	.	43.0	18.0	50.0	0.0	.	183	.	.	Atlas-SNP
LCMT2	9836	hgsc.bcm.edu	hg19	15	43622043	43622043	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	LCMT2	NM_014793	exon1	c.C645G	p.F215L	GACCACGAAAAGG	.	101.0	53.0	256.0	0.0	.	48	.	.	Atlas-SNP
ZNF710	374655	hgsc.bcm.edu	hg19	15	90611162	90611162	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ZNF710	NM_198526	exon2	c.C793T	p.R265C	GTGGAACGCCACA	.	94.0	51.0	196.0	0.0	.	50	.	.	Atlas-SNP
UBN1	29855	hgsc.bcm.edu	hg19	16	4924702	4924702	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	UBN1	NM_001079514	exon15	c.C2291A	p.S764Y	AGCTGTCCTGCCA	.	24.0	4.0	49.0	0.0	.	88	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7577111	7577111	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	TP53_ENST00000455263,NS,NS,0,1	TP53	NM_000546	exon8	c.C827G	p.A276G	GGACAGGCACAAA	.	46.0	41.0	127.0	0.0	.	33396	.	.	Atlas-SNP
OMG	4974	hgsc.bcm.edu	hg19	17	29622317	29622317	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	OMG	NM_002544	exon2	c.T1033A	p.S345T	CATGTGAATTGAT	.	136.0	42.0	170.0	0.0	.	30	.	.	Atlas-SNP
EPB41L3	23136	hgsc.bcm.edu	hg19	18	5428441	5428441	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	EPB41L3	NM_012307	exon9	c.G936C	p.M312I	TCCTAACATAATT	.	79.0	35.0	94.0	0.0	.	222	.	.	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	hg19	19	10475628	10475628	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TYK2	NM_003331	exon8	c.C1108T	p.R370W	GCTCCCGCGGCCT	.	68.0	14.0	95.0	0.0	.	126	.	.	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	hg19	19	44891202	44891202	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	ZNF285,NS,carcinoma,0,2	ZNF285	NM_152354	exon4	c.G1205C	p.C402S	TCACTGCATTTGT	.	53.0	3.0	55.0	1.0	.	86	.	.	Atlas-SNP
BAX	581	hgsc.bcm.edu	hg19	19	49464295	49464295	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	BAX	NM_004324	exon5	c.C598T	p.P200S	TGGTGCCCTCTCC	.	28.0	14.0	22.0	0.0	.	69	.	.	Atlas-SNP
SIGLEC14	100049587	hgsc.bcm.edu	hg19	19	52149062	52149062	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	SIGLEC14,NS,carcinoma,0,2	SIGLEC14	NM_001098612	exon3	c.G673A	p.E225K	TTCTCTCCGTGGT	.	441.0	196.0	695.0	1.0	.	46	.	.	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	hg19	19	56321586	56321586	+	Silent	SNP	G	G	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	NLRP11	NM_145007	exon5	c.C390T	p.Y130Y	AAGTATGTAGAAC	.	107.0	55.0	131.0	0.0	.	139	.	.	Atlas-SNP
BMP2	650	hgsc.bcm.edu	hg19	20	6759153	6759153	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	BMP2	NM_001200	exon3	c.G608T	p.R203M	CAAGCAGGTGGGA	.	96.0	44.0	100.0	0.0	.	45	.	.	Atlas-SNP
CHD6	84181	hgsc.bcm.edu	hg19	20	40045242	40045242	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	CHD6,NS,carcinoma,0,1	CHD6	NM_032221	exon33	c.G6472A	p.A2158T	TCTGGGCCGCCAA	.	64.0	20.0	89.0	0.0	.	312	.	.	Atlas-SNP
PIN4	5303	hgsc.bcm.edu	hg19	X	71401594	71401594	+	Silent	SNP	C	C	A	rs375360841	alternate_allele	TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	PIN4	NM_001170747	exon1	c.C34A	p.R12R	CTTGTACGGCAAC	.	171.0	163.0	243.0	2.0	.	8	.	.	Atlas-SNP
TAF9B	51616	hgsc.bcm.edu	hg19	X	77392438	77392438	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	TAF9B	NM_015975	exon5	c.G455T	p.S152I	TTGCTACTAACAG	.	83.0	5.0	107.0	0.0	.	30	.	.	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	hg19	2	86669229	86669229	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	KDM3A	NM_018433	exon2	c.58delC	p.L20fs	.	.	92.0	58.0	159.0	0.0	.	179	.	.	Atlas-Indel,Pindel
HSP90AB1	3326	hgsc.bcm.edu	hg19	6	44219604	44219604	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	HSP90AB1	NM_001271969	exon9	c.1444delT	p.S482fs	.	.	46.0	30.0	160.0	0.0	.	83	.	.	Atlas-Indel,Pindel
ANKRD12	23253	hgsc.bcm.edu	hg19	18	9255937	9255939	+	In_Frame_Del	DEL	CTG	CTG	-	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	ANKRD12	NM_015208	exon9	c.2671_2673del	p.891_891del	.	.	49.0	12.0	45.0	0.0	.	167	.	.	Atlas-INDEL
HYDIN	54768	hgsc.bcm.edu	hg19	16	70894680	70894680	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A5W4-01A-11D-A28X-10	TCGA-BC-A5W4-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b8ed2260-c9ac-4a92-ae6a-8c6d3ec81274	6f170e0b-fdc4-4cc0-a824-cdd9c60aff16	.	HYDIN	NM_001270974	exon70	c.11903delA	p.E3968fs	.	.	74.0	12.0	65.0	0.0	.	788	.	.	Atlas-INDEL