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
MXRA8	54587	hgsc.bcm.edu	hg19	1	1289296	1289296	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MXRA8	NM_032348	exon9	c.A1235T	p.N412I	AGGATGTTGTTTT	.	83.0	43.0	80.0	0.0	.	28	.	.	Atlas-SNP
ARHGEF10L	55160	hgsc.bcm.edu	hg19	1	17991069	17991069	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ARHGEF10L	NM_018125	exon26	c.A2988C	p.E996D	CCTGGAAGCCACC	.	60.0	28.0	62.0	0.0	.	219	.	.	Atlas-SNP
MAST2	23139	hgsc.bcm.edu	hg19	1	46500283	46500283	+	Silent	SNP	A	A	G	rs139679191	bycluster;by1000genomes;alternate_allele	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MAST2	NM_015112	exon29	c.A3942G	p.T1314T	GCACACACGGCCC	.	300.0	20.0	193.0	0.0	.	136	.	A|0.999;T|0.001	Atlas-SNP
TTC39A	22996	hgsc.bcm.edu	hg19	1	51761791	51761791	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TTC39A	NM_001144832	exon13	c.G1117T	p.D373Y	TGTGGTCCTCCTT	.	60.0	19.0	41.0	0.0	.	40	.	.	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	hg19	1	79412048	79412048	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ELTD1	NM_022159	exon3	c.A236G	p.E79G	CTTCCTTCTGTGT	.	400.0	197.0	443.0	0.0	.	143	.	.	Atlas-SNP
ZNF326	284695	hgsc.bcm.edu	hg19	1	90486427	90486427	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF326	NM_182976	exon10	c.A1251G	p.L417L	TGCTTTACATAGT	.	501.0	221.0	601.0	0.0	.	60	.	.	Atlas-SNP
FAM102B	284611	hgsc.bcm.edu	hg19	1	109148855	109148855	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	FAM102B	NM_001010883	exon3	c.G269C	p.G90A	TAAAAGGTGGAAA	.	283.0	121.0	361.0	0.0	.	49	.	.	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	hg19	1	201046155	201046155	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CACNA1S	NM_000069	exon12	c.G1720A	p.A574T	GGAGGGCGAAGAT	.	646.0	400.0	420.0	1.0	.	249	.	.	Atlas-SNP
CR1	1378	hgsc.bcm.edu	hg19	1	207760833	207760833	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CR1	NM_000651	exon34	c.C5633T	p.P1878L	GCCGTCCTGGGTA	.	534.0	241.0	647.0	1.0	.	354	.	.	Atlas-SNP
ACTN2	88	hgsc.bcm.edu	hg19	1	236881238	236881238	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACTN2	NM_001103	exon2	c.C207A	p.G69G	GAATGGCCTTAAG	.	345.0	155.0	392.0	0.0	.	191	.	.	Atlas-SNP
ACP1	52	hgsc.bcm.edu	hg19	2	277266	277266	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACP1	NM_007099	exon6	c.G439A	p.V147I	CAGTGTGTCAGGT	.	365.0	30.0	400.0	0.0	.	42	.	.	Atlas-SNP
THADA	63892	hgsc.bcm.edu	hg19	2	43813540	43813540	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	THADA	NM_001083953	exon7	c.G533T	p.R178I	ACTTGCCTATTTT	.	475.0	258.0	513.0	1.0	.	131	.	.	Atlas-SNP
EHBP1	23301	hgsc.bcm.edu	hg19	2	63092103	63092103	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	EHBP1	NM_015252	exon10	c.A1100T	p.D367V	AATTGGATGAGTA	.	86.0	36.0	138.0	0.0	.	127	.	.	Atlas-SNP
IL36B	27177	hgsc.bcm.edu	hg19	2	113788640	113788640	+	Missense_Mutation	SNP	G	G	T	rs34754959	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	IL36B	NM_173178	exon3	c.C106A	p.R36S	TGCTGCGGCTAAG	.	129.0	64.0	134.0	0.0	.	69	.	G|0.989;A|0.011	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	hg19	2	142567848	142567848	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	LRP1B	NM_018557	exon2	c.T205A	p.C69S	ACTCACAGGTATC	.	385.0	171.0	554.0	0.0	.	1315	.	.	Atlas-SNP
EPC2	26122	hgsc.bcm.edu	hg19	2	149519486	149519486	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	EPC2	NM_015630	exon5	c.G802T	p.V268F	TTAGAAGTTGTGG	.	347.0	143.0	538.0	0.0	.	57	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179463285	179463285	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TTN	NM_001267550	exon292	c.T57059A	p.V19020E	CCAGTTACTTTGG	.	380.0	156.0	408.0	0.0	.	18412	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179470150	179470150	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TTN	NM_001267550	exon279	c.G53872A	p.D17958N	CATCATCTTGTAT	.	181.0	88.0	245.0	0.0	.	18412	.	.	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	hg19	2	210559239	210559239	+	Missense_Mutation	SNP	C	C	A	rs184529696	bycluster;by1000genomes;alternate_allele	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MAP2	NM_002374	exon7	c.C2345A	p.A782E	CTCAAGCGGAGAT	.	87.0	45.0	110.0	0.0	.	372	.	C|0.994;T|0.006	Atlas-SNP
EPHA4	2043	hgsc.bcm.edu	hg19	2	222347238	222347238	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	EPHA4	NM_004438	exon5	c.C1152A	p.V384V	GTAGTGGACCCCA	.	293.0	133.0	363.0	0.0	.	263	.	.	Atlas-SNP
SP110	3431	hgsc.bcm.edu	hg19	2	231079722	231079722	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SP110	NM_001185015	exon4	c.C277G	p.Q93E	TAATTTGACTGAA	.	232.0	102.0	233.0	0.0	.	105	.	.	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	hg19	3	430967	430967	+	Silent	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CHL1	NM_001253388	exon18	c.C2280G	p.G760G	ACCAGGCCTAGAG	.	159.0	69.0	187.0	0.0	.	242	.	.	Atlas-SNP
GADL1	339896	hgsc.bcm.edu	hg19	3	30827849	30827849	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	GADL1	NM_207359	exon13	c.G1300T	p.E434X	TTACTTCCATCAG	.	292.0	127.0	313.0	0.0	.	91	.	.	Atlas-SNP
KIF9	64147	hgsc.bcm.edu	hg19	3	47307360	47307360	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	KIF9,NS,adenoma,0,1	KIF9	NM_182902	exon8	c.G776A	p.G259D	ACTTGGCCCTCAG	.	144.0	66.0	192.0	1.0	.	59	.	.	Atlas-SNP
EPHA6	285220	hgsc.bcm.edu	hg19	3	96706423	96706423	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	EPHA6	NM_001080448	exon3	c.T700G	p.F234V	ATTAAATTCAAGC	.	153.0	80.0	190.0	0.0	.	439	.	.	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	hg19	3	121251856	121251856	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	POLQ	NM_199420	exon6	c.A941G	p.E314G	ATGGGCTCAAATT	.	495.0	229.0	523.0	0.0	.	273	.	.	Atlas-SNP
PDS5A	23244	hgsc.bcm.edu	hg19	4	39928476	39928476	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PDS5A	NM_001100399	exon4	c.A348G	p.I116M	CAAAAATATGTCC	.	180.0	79.0	278.0	0.0	.	114	.	.	Atlas-SNP
GABRG1	2565	hgsc.bcm.edu	hg19	4	46060339	46060339	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	GABRG1	NM_173536	exon7	c.G811T	p.G271X	AATATCCCATTCT	.	445.0	192.0	645.0	1.0	.	172	.	.	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	hg19	4	104079539	104079539	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CENPE	NM_001813	exon24	c.A2951T	p.K984I	TTCGATTTTAGTG	.	90.0	77.0	279.0	0.0	.	253	.	.	Atlas-SNP
C4orf45	152940	hgsc.bcm.edu	hg19	4	159894436	159894436	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	C4orf45	NM_152543	exon2	c.C92A	p.P31H	ATTTTGGGTAAAT	.	223.0	100.0	270.0	0.0	.	8	.	.	Atlas-SNP
C4orf45	152940	hgsc.bcm.edu	hg19	4	159894437	159894437	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	C4orf45	NM_152543	exon2	c.C91A	p.P31T	TTTTGGGTAAATA	.	221.0	98.0	263.0	0.0	.	8	.	.	Atlas-SNP
WDR41	55255	hgsc.bcm.edu	hg19	5	76785371	76785371	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	WDR41	NM_018268	exon2	c.A78T	p.E26D	TTGTTCTTCACCT	.	350.0	164.0	378.0	0.0	.	29	.	.	Atlas-SNP
POU5F2	134187	hgsc.bcm.edu	hg19	5	93076516	93076516	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	POU5F2	NM_153216	exon1	c.G754C	p.D252H	CCACATCCTTCTG	.	251.0	117.0	257.0	0.0	.	10	.	.	Atlas-SNP
LNPEP	4012	hgsc.bcm.edu	hg19	5	96332096	96332096	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	LNPEP	NM_005575	exon7	c.G1410T	p.W470C	CCAGTGGTTTGGC	.	345.0	178.0	456.0	0.0	.	80	.	.	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	hg19	5	101816070	101816070	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SLCO6A1	NM_173488	exon2	c.G427C	p.E143Q	ACTTCTCAATGGT	.	368.0	169.0	486.0	0.0	.	153	.	.	Atlas-SNP
APC	324	hgsc.bcm.edu	hg19	5	112177044	112177044	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	APC	NM_001127510	exon17	c.T5753C	p.I1918T	AGCCAATAAATCG	.	267.0	134.0	254.0	0.0	.	4158	.	.	Atlas-SNP
PRR16	51334	hgsc.bcm.edu	hg19	5	120022379	120022379	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PRR16	NM_016644	exon3	c.G821T	p.R274M	TCTTGAGGAAGTC	.	25.0	15.0	20.0	0.0	.	71	.	.	Atlas-SNP
PRR16	51334	hgsc.bcm.edu	hg19	5	120022380	120022380	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	PRR16,NS,carcinoma,0,1	PRR16	NM_016644	exon3	c.G822T	p.R274S	CTTGAGGAAGTCA	.	25.0	15.0	20.0	0.0	.	71	.	.	Atlas-SNP
PSD2	84249	hgsc.bcm.edu	hg19	5	139189077	139189077	+	Missense_Mutation	SNP	C	C	T	rs146689892		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PSD2	NM_032289	exon2	c.C52T	p.R18C	GCCACCCGTGACC	.	139.0	63.0	122.0	0.0	.	88	.	C|1.000;T|0.000	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	hg19	5	158603765	158603765	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	RNF145	NM_001199380	exon5	c.G586T	p.E196X	TTGTCTCCAAAGG	.	788.0	317.0	873.0	1.0	.	110	.	.	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	hg19	5	158603766	158603766	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	RNF145	NM_001199380	exon5	c.G585T	p.L195F	TGTCTCCAAAGGA	.	785.0	317.0	868.0	2.0	.	110	.	.	Atlas-SNP
GNB2L1	10399	hgsc.bcm.edu	hg19	5	180666567	180666567	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	GNB2L1	NM_006098	exon4	c.G445C	p.E149Q	CCCACTCTGAGTG	.	94.0	43.0	106.0	0.0	.	22	.	.	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	hg19	6	43517661	43517661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	XPO5	NM_020750	exon16	c.C1739T	p.S580F	GTGACAGATGAAA	.	264.0	160.0	181.0	0.0	.	79	.	.	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	hg19	6	117198538	117198538	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	RFX6	NM_173560	exon1	c.G100A	p.G34S	CTCCTGGGCAAGG	.	108.0	49.0	63.0	0.0	.	141	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152765606	152765606	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SYNE1	NM_033071	exon30	c.T3798A	p.A1266A	CTTCTCAGCTTGT	.	253.0	120.0	310.0	0.0	.	3227	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152765624	152765624	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SYNE1	NM_033071	exon30	c.A3780C	p.K1260N	GACTTCTTTAGAG	.	255.0	115.0	329.0	0.0	.	3227	.	.	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	hg19	7	2979547	2979547	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CARD11	NM_032415	exon6	c.C700T	p.H234Y	ACCGGTGCTTTAG	.	350.0	169.0	422.0	0.0	.	339	.	.	Atlas-SNP
WIPF3	644150	hgsc.bcm.edu	hg19	7	29923639	29923639	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	WIPF3	NM_001080529	exon5	c.C529G	p.P177A	CCCCCTCCCACCC	.	31.0	14.0	13.0	0.0	.	46	.	.	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	hg19	7	31683115	31683115	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CCDC129	NM_001257968	exon11	c.C2209A	p.Q737K	ATGACCCAGATGT	.	189.0	93.0	190.0	0.0	.	127	.	.	Atlas-SNP
GPR141	353345	hgsc.bcm.edu	hg19	7	37780403	37780403	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	GPR141	NM_181791	exon1	c.T408C	p.S136S	TGCCAGTGCTGGC	.	258.0	108.0	314.0	1.0	.	79	.	.	Atlas-SNP
NPC1L1	29881	hgsc.bcm.edu	hg19	7	44579861	44579861	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NPC1L1	NM_001101648	exon2	c.G135A	p.L45L	TCCAGACAGCTCT	.	122.0	49.0	115.0	0.0	.	141	.	.	Atlas-SNP
WBSCR17	64409	hgsc.bcm.edu	hg19	7	71130478	71130478	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	WBSCR17	NM_022479	exon7	c.G1163T	p.S388I	ATAATAGCAACAT	.	188.0	96.0	137.0	0.0	.	208	.	.	Atlas-SNP
ZKSCAN1	7586	hgsc.bcm.edu	hg19	7	99621227	99621227	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZKSCAN1	NM_003439	exon2	c.A98T	p.E33V	AAGATGAGGAAGA	.	96.0	36.0	117.0	0.0	.	59	.	.	Atlas-SNP
DUS4L	11062	hgsc.bcm.edu	hg19	7	107216972	107216972	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DUS4L	NM_001270419	exon7	c.T641C	p.I214T	CTGTAATTGCTAA	.	179.0	81.0	246.0	0.0	.	27	.	.	Atlas-SNP
CHRM2	1129	hgsc.bcm.edu	hg19	7	136699983	136699983	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CHRM2	NM_001006632	exon3	c.G371T	p.C124F	ACTTCTGTGTCAC	.	315.0	160.0	389.0	1.0	.	167	.	.	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	hg19	7	141731507	141731507	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MGAM	NM_004668	exon13	c.G1498T	p.D500Y	TTTCCTGATTATA	.	396.0	171.0	463.0	0.0	.	767	.	.	Atlas-SNP
DEFA4	1669	hgsc.bcm.edu	hg19	8	6793612	6793612	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DEFA4	NM_001925	exon3	c.C224G	p.T75R	AGTTCTGTTCGCC	.	102.0	45.0	67.0	0.0	.	19	.	.	Atlas-SNP
SGK223	0	hgsc.bcm.edu	hg19	8	8185737	8185737	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	NM_001080826	exon4	c.C2555A	p.T852N	ACGTTGGTTTCCG	.	88.0	43.0	72.0	0.0	.	.	.	.	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	hg19	8	17794745	17794745	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PCM1	NM_006197	exon4	c.G199A	p.E67K	TCTCCGGAGTCGT	.	281.0	130.0	345.0	0.0	.	120	.	.	Atlas-SNP
BAG4	9530	hgsc.bcm.edu	hg19	8	38067967	38067967	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	BAG4	NM_004874	exon5	c.A1330C	p.K444Q	GTTTGTAAGATTC	.	135.0	54.0	168.0	0.0	.	32	.	.	Atlas-SNP
CSPP1	79848	hgsc.bcm.edu	hg19	8	68105731	68105731	+	Silent	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CSPP1	NM_024790	exon28	c.T3348G	p.G1116G	AGATGGTCTCTCT	.	213.0	98.0	221.0	0.0	.	129	.	.	Atlas-SNP
NECAB1	64168	hgsc.bcm.edu	hg19	8	91946573	91946573	+	Silent	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NECAB1	NM_022351	exon9	c.G735C	p.G245G	TGAAGGGAATACT	.	341.0	126.0	581.0	0.0	.	31	.	.	Atlas-SNP
ANKRD46	157567	hgsc.bcm.edu	hg19	8	101540171	101540171	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ANKRD46	NM_001270378	exon4	c.C372T	p.V124V	TCGGATGACATCT	.	270.0	112.0	374.0	1.0	.	13	.	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	hg19	8	113519006	113519006	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CSMD3	NM_198123	exon29	c.C4809A	p.N1603K	AGGGAAGTTTGGT	.	280.0	112.0	290.0	0.0	.	2325	.	.	Atlas-SNP
MYC	4609	hgsc.bcm.edu	hg19	8	128751001	128751001	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MYC	NM_002467	exon2	c.G538A	p.A180T	AACCCCGCCCGCG	.	44.0	27.0	29.0	0.0	.	168	.	.	Atlas-SNP
C8orf31	286122	hgsc.bcm.edu	hg19	8	144124680	144124680	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	C8orf31	NM_173687	exon3	c.186+1G>A	.	GCACTTGTAAGTT	.	29.0	11.0	27.0	0.0	.	18	.	.	Atlas-SNP
RHPN1	114822	hgsc.bcm.edu	hg19	8	144460480	144460480	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	RHPN1	NM_052924	exon5	c.C423T	p.Y141Y	CTCCTACGAGGCA	.	77.0	37.0	59.0	0.0	.	76	.	.	Atlas-SNP
GSDMD	79792	hgsc.bcm.edu	hg19	8	144644198	144644198	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	GSDMD	NM_001166237	exon11	c.C893G	p.S298C	CCATCTCCAAGGA	.	35.0	17.0	26.0	0.0	.	28	.	.	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	hg19	9	14816837	14816837	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	FREM1	NM_144966	exon16	c.A2579G	p.D860G	AGGTCATCCTGAA	.	69.0	20.0	63.0	0.0	.	261	.	.	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	hg19	9	35697837	35697837	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TLN1	NM_006289	exon57	c.G7577A	p.R2526Q	TGCTGCCGGATCT	.	550.0	187.0	426.0	0.0	.	185	.	.	Atlas-SNP
TMEM8B	51754	hgsc.bcm.edu	hg19	9	35841793	35841793	+	Splice_Site	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TMEM8B	.	.	.	.	GCAAGGTCAGAAC	.	210.0	87.0	203.0	0.0	.	53	.	.	Atlas-SNP
ZNF510	22869	hgsc.bcm.edu	hg19	9	99522164	99522164	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF510	NM_014930	exon6	c.A948G	p.K316K	AAAGGATTTCCCA	.	215.0	110.0	297.0	0.0	.	59	.	.	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	hg19	9	107584777	107584777	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ABCA1	NM_005502	exon19	c.T2828C	p.M943T	TCTTACATGGTGG	.	86.0	43.0	107.0	0.0	.	244	.	.	Atlas-SNP
PTPN3	5774	hgsc.bcm.edu	hg19	9	112185130	112185130	+	Missense_Mutation	SNP	G	G	A	rs376647767		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PTPN3	NM_002829	exon13	c.C1004T	p.S335L	TTTACCGACCTGA	.	169.0	54.0	193.0	0.0	.	106	.	.	Atlas-SNP
OR1L8	138881	hgsc.bcm.edu	hg19	9	125329852	125329852	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	OR1L8	NM_001004454	exon1	c.G905T	p.R302M	AGCTTCCTCAGGC	.	102.0	46.0	156.0	0.0	.	90	.	.	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	hg19	9	139904510	139904510	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ABCA2	NM_212533	exon42	c.C6510T	p.F2170F	CTCGTCGAACAGC	.	39.0	19.0	37.0	0.0	.	113	.	.	Atlas-SNP
PRKG1	5592	hgsc.bcm.edu	hg19	10	54048601	54048601	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	PRKG1_ENST00000401604,colon,carcinoma,0,2	PRKG1	NM_006258	exon15	c.C1825T	p.L609L	AAAAAACTATGCA	.	135.0	64.0	229.0	0.0	.	167	.	.	Atlas-SNP
SLC16A9	220963	hgsc.bcm.edu	hg19	10	61413875	61413875	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SLC16A9	NM_194298	exon5	c.C909A	p.N303K	TACTTTGTTTTTA	.	191.0	90.0	268.0	0.0	.	58	.	.	Atlas-SNP
HK1	3098	hgsc.bcm.edu	hg19	10	71136836	71136836	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	HK1	NM_033498	exon11	c.C1034T	p.A345V	TGTCAGCCATCGA	.	95.0	36.0	127.0	0.0	.	170	.	.	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	hg19	10	134660574	134660574	+	Silent	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TTC40	NM_001200049	exon43	c.A6129T	p.S2043S	CACCTCTGACGCC	.	31.0	11.0	41.0	0.0	.	100	.	.	Atlas-SNP
OR51V1	283111	hgsc.bcm.edu	hg19	11	5221902	5221902	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	OR51V1	NM_001004760	exon1	c.C29T	p.S10L	CTTACTGAAGTAA	.	121.0	54.0	164.0	0.0	.	77	.	.	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	hg19	11	6477958	6477958	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TRIM3	NM_001248006	exon6	c.G998T	p.R333L	GCCTGGCGCAGGC	.	76.0	29.0	56.0	0.0	.	67	.	.	Atlas-SNP
MRVI1	10335	hgsc.bcm.edu	hg19	11	10651167	10651167	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MRVI1	NM_001206880	exon5	c.G492T	p.L164L	TTCTTCCAGCAGC	.	340.0	158.0	353.0	0.0	.	113	.	.	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	hg19	11	46896621	46896621	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	LRP4	NM_002334	exon28	c.G3959A	p.C1320Y	TGGGAGCAGCCGC	.	51.0	16.0	51.0	0.0	.	160	.	.	Atlas-SNP
OR4C3	256144	hgsc.bcm.edu	hg19	11	48346884	48346884	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	OR4C3	NM_001004702	exon1	c.T392G	p.F131C	CTCATTTTTTGGG	.	857.0	163.0	992.0	1.0	.	75	.	.	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	hg19	11	51412172	51412172	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	OR4A5	NM_001005272	exon1	c.T224C	p.I75T	GGAGAAATGGTAG	.	430.0	188.0	482.0	0.0	.	116	.	.	Atlas-SNP
OR5B17	219965	hgsc.bcm.edu	hg19	11	58125852	58125852	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	OR5B17,NS,adenoma,0,1	OR5B17	NM_001005489	exon1	c.G691C	p.G231R	GGTATCCCTTACC	.	91.0	43.0	147.0	0.0	.	64	.	.	Atlas-SNP
TYR	7299	hgsc.bcm.edu	hg19	11	88911272	88911272	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	TYR,NS,carcinoma,-1,1	TYR	NM_000372	exon1	c.G151A	p.G51S	CTTTCAGGCAGAG	.	98.0	32.0	112.0	0.0	.	130	.	.	Atlas-SNP
ST14	6768	hgsc.bcm.edu	hg19	11	130058534	130058534	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ST14	NM_021978	exon3	c.C351T	p.A117A	CCTGGCCAGCAAG	.	89.0	37.0	62.0	0.0	.	82	.	.	Atlas-SNP
TMPRSS12	283471	hgsc.bcm.edu	hg19	12	51237659	51237659	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TMPRSS12	NM_182559	exon2	c.A222G	p.Q74Q	GTTGCAAGGGTCT	.	132.0	63.0	153.0	0.0	.	33	.	.	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	hg19	12	52822123	52822123	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KRT75	NM_004693	exon7	c.G1299T	p.E433D	CTGGTACTCACGC	.	104.0	50.0	108.0	0.0	.	75	.	.	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	hg19	12	52841356	52841356	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KRT6B	NM_005555	exon8	c.C1426T	p.L476L	CATTCAGCCTGTG	.	205.0	90.0	219.0	0.0	.	90	.	.	Atlas-SNP
AMHR2	269	hgsc.bcm.edu	hg19	12	53823987	53823987	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	AMHR2	NM_020547	exon10	c.C1346A	p.T449N	CCCCTACCTCTGA	.	218.0	110.0	219.0	0.0	.	61	.	.	Atlas-SNP
HOXC10	3226	hgsc.bcm.edu	hg19	12	54382961	54382961	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	HOXC10	NM_017409	exon2	c.A760G	p.K254E	GAGATAAAGGCAG	.	127.0	61.0	174.0	0.0	.	42	.	.	Atlas-SNP
CCDC59	29080	hgsc.bcm.edu	hg19	12	82752141	82752141	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CCDC59	NM_014167	exon1	c.G15T	p.R5S	GGACCGCCTCACC	.	53.0	24.0	38.0	0.0	.	17	.	.	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	hg19	12	85546125	85546125	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	LRRIQ1	NM_001079910	exon20	c.C4397A	p.S1466X	TTCTTTCAAACCA	.	225.0	102.0	253.0	0.0	.	512	.	.	Atlas-SNP
DUSP6	1848	hgsc.bcm.edu	hg19	12	89744457	89744457	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DUSP6	NM_001946	exon2	c.A746G	p.N249S	CCTGCGTTCTCAA	.	165.0	72.0	206.0	0.0	.	30	.	.	Atlas-SNP
ANO4	121601	hgsc.bcm.edu	hg19	12	101491695	101491695	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ANO4	NM_178826	exon20	c.T1873A	p.W625R	CAGACCTGGAATA	.	231.0	112.0	316.0	0.0	.	183	.	.	Atlas-SNP
ACACB	32	hgsc.bcm.edu	hg19	12	109637346	109637346	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACACB	NM_001093	exon17	c.G2767C	p.A923P	AGCTACGCTGAGA	.	31.0	26.0	54.0	0.0	.	330	.	.	Atlas-SNP
ACACB	32	hgsc.bcm.edu	hg19	12	109637347	109637347	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACACB	NM_001093	exon17	c.C2768T	p.A923V	GCTACGCTGAGAT	.	31.0	24.0	53.0	0.0	.	330	.	.	Atlas-SNP
NAA25	80018	hgsc.bcm.edu	hg19	12	112499100	112499100	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NAA25	NM_024953	exon12	c.T1242A	p.H414Q	ACACAAATGTTGC	.	202.0	95.0	163.0	0.0	.	105	.	.	Atlas-SNP
PITPNM2	57605	hgsc.bcm.edu	hg19	12	123474487	123474487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PITPNM2	NM_020845	exon17	c.G2578T	p.D860Y	GCGCATCGGGGGC	.	20.0	9.0	15.0	0.0	.	105	.	.	Atlas-SNP
PITPNM2	57605	hgsc.bcm.edu	hg19	12	123497236	123497236	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	PITPNM2,NS,carcinoma,0,1	PITPNM2	NM_020845	exon4	c.C339T	p.T113T	ATAAAAGGTTTCA	.	116.0	48.0	145.0	0.0	.	105	.	.	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	hg19	13	24797411	24797411	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SPATA13	NM_001166271	exon2	c.A344T	p.K115M	CCTTTAAGAAACT	.	58.0	27.0	45.0	0.0	.	92	.	.	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	hg19	13	33017687	33017687	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	N4BP2L2	NM_033111	exon7	c.A987G	p.K329K	GAGATTTTTATCT	.	331.0	175.0	379.0	0.0	.	90	.	.	Atlas-SNP
POSTN	10631	hgsc.bcm.edu	hg19	13	38164531	38164531	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	POSTN	NM_006475	exon4	c.A419T	p.E140V	CAAGCCTCATTAC	.	57.0	23.0	93.0	0.0	.	161	.	.	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	hg19	13	42293771	42293771	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	NM_015058	exon26	c.G3072T	p.G1024G	AGGTATCCCGTAT	.	312.0	120.0	307.0	0.0	.	.	.	.	Atlas-SNP
JPH4	84502	hgsc.bcm.edu	hg19	14	24040535	24040535	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	JPH4	NM_001146028	exon5	c.C1405T	p.Q469X	AGGGTTGGCGGGA	.	48.0	21.0	51.0	0.0	.	64	.	.	Atlas-SNP
CLEC14A	161198	hgsc.bcm.edu	hg19	14	38724364	38724364	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CLEC14A	NM_175060	exon1	c.C864T	p.T288T	CCCACTGGTCACA	.	35.0	9.0	35.0	0.0	.	83	.	.	Atlas-SNP
CLEC14A	161198	hgsc.bcm.edu	hg19	14	38724365	38724365	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CLEC14A	NM_175060	exon1	c.C863A	p.T288N	CCACTGGTCACAC	.	35.0	9.0	33.0	0.0	.	83	.	.	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	hg19	14	68274384	68274384	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZFYVE26	NM_015346	exon5	c.G617A	p.G206D	TCAGGGCCCTGCA	.	19.0	13.0	40.0	0.0	.	223	.	.	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	hg19	14	69350972	69350972	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACTN1	NM_001102	exon14	c.G1548T	p.K516N	AGCCCGCTTGGCA	.	122.0	111.0	251.0	1.0	.	77	.	.	Atlas-SNP
ACTN1	87	hgsc.bcm.edu	hg19	14	69350974	69350974	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACTN1	NM_001102	exon14	c.A1546G	p.K516E	CCCGCTTGGCATA	.	122.0	110.0	260.0	0.0	.	77	.	.	Atlas-SNP
ACOT2	10965	hgsc.bcm.edu	hg19	14	74036182	74036182	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ACOT2	NM_006821	exon1	c.C238A	p.P80T	GACGAACCGGTGC	.	47.0	41.0	61.0	0.0	.	24	.	.	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	hg19	14	102478246	102478246	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DYNC1H1	NM_001376	exon33	c.A6653T	p.H2218L	TCAATCATGGCCT	.	118.0	61.0	131.0	0.0	.	395	.	.	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	hg19	15	42734378	42734378	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZFP106	NM_022473	exon7	c.C3587T	p.S1196L	TGAACTGATGAGT	.	241.0	116.0	262.0	0.0	.	117	.	.	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	hg19	15	45713263	45713263	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SPATA5L1	NM_024063	exon8	c.A2117G	p.E706G	TGCAAGAAAATGG	.	84.0	41.0	99.0	0.0	.	40	.	.	Atlas-SNP
FBN1	2200	hgsc.bcm.edu	hg19	15	48796007	48796007	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	FBN1	NM_000138	exon17	c.A2090C	p.Q697P	CACGGCTGGCAAG	.	223.0	96.0	259.0	1.0	.	310	.	.	Atlas-SNP
ISL2	64843	hgsc.bcm.edu	hg19	15	76632729	76632729	+	Silent	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ISL2	NM_145805	exon4	c.C624G	p.T208T	GCGGACCTGCTAC	.	125.0	28.0	77.0	0.0	.	20	.	.	Atlas-SNP
BTBD1	53339	hgsc.bcm.edu	hg19	15	83687553	83687553	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	BTBD1	NM_025238	exon7	c.G1196A	p.S399N	TCACAACTAAAGC	.	332.0	166.0	388.0	0.0	.	32	.	.	Atlas-SNP
CDIPT	10423	hgsc.bcm.edu	hg19	16	29873915	29873915	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CDIPT	NM_006319	exon2	c.T170C	p.L57P	TGATTAAGAGCGC	.	138.0	63.0	124.0	0.0	.	15	.	.	Atlas-SNP
SLC6A2	6530	hgsc.bcm.edu	hg19	16	55736246	55736246	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SLC6A2	NM_001172501	exon15	c.G1842T	p.W614C	ACACTGGCTGGCC	.	150.0	141.0	298.0	1.0	.	189	.	.	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	hg19	17	15973501	15973501	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NCOR1	NM_001190440	exon30	c.C4539A	p.P1513P	CATCATGGGTGAG	.	84.0	68.0	154.0	0.0	.	240	.	.	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	hg19	17	28295950	28295950	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	EFCAB5	NM_198529	exon4	c.A332G	p.E111G	AGCCAGAGCACAC	.	213.0	113.0	242.0	1.0	.	122	.	.	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	hg19	17	32959819	32959819	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	TMEM132E,NS,carcinoma,0,1	TMEM132E	NM_207313	exon7	c.C1309T	p.P437S	AATGCTCCCCTGG	.	262.0	74.0	190.0	0.0	.	122	.	.	Atlas-SNP
LYZL6	57151	hgsc.bcm.edu	hg19	17	34261843	34261843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	LYZL6	NM_020426	exon4	c.G404T	p.G135V	GGCCGGCCTGAAC	.	115.0	69.0	65.0	0.0	.	18	.	.	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	hg19	17	35880688	35880688	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SYNRG	NM_007247	exon20	c.G3730C	p.E1244Q	CAAGCTCCTGAGC	.	208.0	71.0	158.0	0.0	.	101	.	.	Atlas-SNP
FBXO47	494188	hgsc.bcm.edu	hg19	17	37093476	37093476	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	FBXO47	NM_001008777	exon11	c.C1311A	p.F437L	CTTATGGAAGTTA	.	278.0	165.0	183.0	0.0	.	34	.	.	Atlas-SNP
STARD3	10948	hgsc.bcm.edu	hg19	17	37814042	37814042	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	STARD3	NM_006804	exon4	c.C312T	p.F104F	CTTCTTCCGCTTC	.	427.0	254.0	284.0	0.0	.	33	.	.	Atlas-SNP
KRT34	3885	hgsc.bcm.edu	hg19	17	39534380	39534380	+	Nonsense_Mutation	SNP	G	G	T	rs138365209	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KRT34	NM_021013	exon7	c.C1242A	p.C414X	GGTGGCGCATGGG	.	175.0	60.0	114.0	0.0	.	71	.	G|0.999;A|0.001	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	hg19	17	66303755	66303755	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ARSG	NM_001267727	exon2	c.A121G	p.I41V	GTGATTATTTTGG	.	753.0	241.0	519.0	0.0	.	55	.	.	Atlas-SNP
HID1	283987	hgsc.bcm.edu	hg19	17	72949120	72949120	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	NM_030630	exon16	c.G2033A	p.W678X	GGGCTCCACTGCC	.	256.0	83.0	124.0	0.0	.	.	.	.	Atlas-SNP
TEX19	400629	hgsc.bcm.edu	hg19	17	80320463	80320463	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TEX19	NM_207459	exon2	c.C437G	p.P146R	GTCTTCCCTGGAG	.	215.0	68.0	160.0	0.0	.	17	.	.	Atlas-SNP
CCBE1	147372	hgsc.bcm.edu	hg19	18	57364549	57364549	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CCBE1	NM_133459	exon1	c.G26T	p.G9V	GCTCCTCCCCGGC	.	52.0	25.0	32.0	0.0	.	59	.	.	Atlas-SNP
DOT1L	84444	hgsc.bcm.edu	hg19	19	2217053	2217053	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DOT1L	NM_032482	exon21	c.G2508A	p.G836G	CCCTGGGGCCTTG	.	43.0	17.0	39.0	0.0	.	205	.	.	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	hg19	19	2989558	2989558	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TLE6	NM_001143986	exon13	c.G1019A	p.C340Y	GCACCTGCCTGCT	.	49.0	15.0	67.0	0.0	.	68	.	.	Atlas-SNP
TIMM44	10469	hgsc.bcm.edu	hg19	19	7996055	7996055	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TIMM44	NM_006351	exon10	c.C1006G	p.L336V	TGTCAAGCTCTCC	.	271.0	89.0	370.0	1.0	.	47	.	.	Atlas-SNP
ELAVL1	1994	hgsc.bcm.edu	hg19	19	8028565	8028565	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ELAVL1	NM_001419	exon6	c.G783T	p.W261C	CATCTGCCAGAGG	.	194.0	105.0	247.0	0.0	.	44	.	.	Atlas-SNP
FDX1L	112812	hgsc.bcm.edu	hg19	19	10426560	10426560	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	FDX1L	NM_001031734	exon1	c.C113T	p.A38V	CCCAGCGCCACCC	.	71.0	28.0	79.0	0.0	.	21	.	.	Atlas-SNP
CALR	811	hgsc.bcm.edu	hg19	19	13054680	13054680	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	CALR,NS,lymphoid_neoplasm,0,1	CALR	NM_004343	exon9	c.G1207T	p.E403X	AAGGAGGAAGATG	.	388.0	193.0	424.0	1.0	.	31	.	.	Atlas-SNP
CC2D1A	54862	hgsc.bcm.edu	hg19	19	14038069	14038069	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CC2D1A	NM_017721	exon22	c.G2307A	p.E769E	CCGGGAGATCCTT	.	221.0	9.0	217.0	0.0	.	67	.	.	Atlas-SNP
ZNF486	90649	hgsc.bcm.edu	hg19	19	20308237	20308237	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF486	NM_052852	exon4	c.T718C	p.C240R	TACAAATGTGAAG	.	93.0	52.0	94.0	0.0	.	74	.	.	Atlas-SNP
ZNF429	353088	hgsc.bcm.edu	hg19	19	21720692	21720692	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF429	NM_001001415	exon4	c.A1837T	p.K613X	CATAAGAAAATTC	.	102.0	45.0	90.0	0.0	.	338	.	.	Atlas-SNP
SERTAD1	29950	hgsc.bcm.edu	hg19	19	40929016	40929016	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SERTAD1	NM_013376	exon2	c.G438T	p.G146G	TGCTCCCCCGATG	.	40.0	19.0	56.0	0.0	.	18	.	.	Atlas-SNP
POU2F2	5452	hgsc.bcm.edu	hg19	19	42636560	42636560	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	POU2F2	NM_002698	exon1	c.G4T	p.V2F	AGTGAACCATGCT	.	92.0	42.0	69.0	0.0	.	106	.	.	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	hg19	19	44890851	44890851	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF285	NM_152354	exon4	c.A1556C	p.K519T	AAGCCTTTACCAC	.	422.0	204.0	501.0	0.0	.	86	.	.	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	hg19	19	49248991	49248991	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	IZUMO1	NM_182575	exon2	c.T126C	p.P42P	GTGGCCAGGCAGG	.	356.0	161.0	378.0	0.0	.	30	.	.	Atlas-SNP
IL4I1	259307	hgsc.bcm.edu	hg19	19	50393089	50393089	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	IL4I1	NM_172374	exon10	c.G1608A	p.T536T	GCTGGCCGTGTCC	.	147.0	6.0	155.0	0.0	.	50	.	.	Atlas-SNP
KLK6	5653	hgsc.bcm.edu	hg19	19	51465087	51465087	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KLK6	NM_001012964	exon5	c.T495A	p.R165R	CTCCTCACGGGAC	.	149.0	65.0	121.0	0.0	.	35	.	.	Atlas-SNP
KLK8	11202	hgsc.bcm.edu	hg19	19	51503358	51503358	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KLK8	NM_144505	exon4	c.G522A	p.Q174Q	GGATGCCTGGTCA	.	97.0	53.0	108.0	0.0	.	46	.	.	Atlas-SNP
SIGLEC8	27181	hgsc.bcm.edu	hg19	19	51961640	51961640	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SIGLEC8	NM_014442	exon1	c.T2A	p.M1K	AGCAGCATGTCTG	.	124.0	55.0	102.0	0.0	.	130	.	.	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	hg19	20	50701265	50701265	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZFP64	NM_199427	exon9	c.T1769G	p.V590G	TCCCTGACGAAGG	.	93.0	52.0	75.0	0.0	.	240	.	.	Atlas-SNP
PMEPA1	56937	hgsc.bcm.edu	hg19	20	56227370	56227370	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	PMEPA1	NM_020182	exon4	c.G603A	p.R201R	GCCCAGCCTGGCA	.	34.0	20.0	17.0	0.0	.	29	.	.	Atlas-SNP
SS18L1	26039	hgsc.bcm.edu	hg19	20	60747838	60747838	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	SS18L1_ENST00000331758,right_upper_lobe,carcinoma,0,1	SS18L1	NM_198935	exon9	c.C1017T	p.P339P	CTACCCCGGGCAG	.	94.0	4.0	78.0	0.0	.	37	.	.	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	hg19	20	62839764	62839764	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MYT1	NM_004535	exon7	c.G1215T	p.Q405H	CGAGCAGAGCCAG	.	63.0	25.0	53.0	0.0	.	152	.	.	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	hg19	21	41505791	41505791	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	DSCAM	NM_001271534	exon19	c.C3552A	p.T1184T	CTCTTTGGTCCGG	.	146.0	59.0	159.0	0.0	.	347	.	.	Atlas-SNP
CABIN1	23523	hgsc.bcm.edu	hg19	22	24472172	24472172	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CABIN1	NM_001199281	exon19	c.A2687T	p.H896L	CAGCCCACGAGTA	.	297.0	147.0	270.0	0.0	.	153	.	.	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	hg19	22	26423432	26423432	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MYO18B	NM_032608	exon43	c.C7492T	p.P2498S	CCGGAGCCCAAGG	.	66.0	33.0	68.0	0.0	.	322	.	.	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	hg19	22	31487025	31487025	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SMTN	NM_001207018	exon9	c.C1184G	p.S395C	TCACATCTGATTC	.	261.0	109.0	247.0	0.0	.	219	.	.	Atlas-SNP
CNKSR2	22866	hgsc.bcm.edu	hg19	X	21627708	21627708	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CNKSR2	NM_014927	exon20	c.G2665T	p.A889S	GGGGAGGCAGCAG	.	29.0	21.0	22.0	0.0	.	158	.	.	Atlas-SNP
AR	367	hgsc.bcm.edu	hg19	X	66766453	66766453	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	AR	NM_000044	exon1	c.G1465A	p.G489R	CCTCAGGGGCTGG	.	53.0	22.0	48.0	0.0	.	249	.	.	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6675	6675	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	ENST00000361624	exon1	c.G772A	p.V258M	CATATTGTAACTT	.	237.0	109.0	425.0	0.0	.	.	.	.	Atlas-SNP
ND5	0	hgsc.bcm.edu	hg19	MT	13597	13597	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	ENST00000361567	exon1	c.G1261A	p.A421T	ACAAGCGCCTATA	.	202.0	15.0	369.0	0.0	.	.	.	.	Atlas-SNP
NLGN1	22871	hgsc.bcm.edu	hg19	3	173993239	173993239	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NLGN1	NM_014932	exon5	c.780delT	p.S260fs	.	.	316.0	96.0	264.0	0.0	.	209	.	.	Atlas-INDEL
NCOR1	9611	hgsc.bcm.edu	hg19	17	15973499	15973499	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NCOR1	NM_001190440	exon30	c.4542delG	p.M1514fs	.	.	82.0	69.0	150.0	0.0	.	240	.	.	Atlas-INDEL
KIF19	124602	hgsc.bcm.edu	hg19	17	72345442	72345442	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KIF19	NM_153209	exon10	c.1166delG	p.G389fs	.	.	166.0	96.0	127.0	0.0	.	102	.	.	Atlas-Indel,Pindel
KCNU1	157855	hgsc.bcm.edu	hg19	8	36691164	36691173	+	Frame_Shift_Del	DEL	TGAGGCGAGT	TGAGGCGAGT	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	TGAGGCGAGT	TGAGGCGAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	KCNU1	NM_001031836	exon11	c.1198_1207del	p.400_403del	.	.	391.0	116.0	688.0	0.0	.	359	.	.	Atlas-Indel,Pindel
AP3M2	10947	hgsc.bcm.edu	hg19	8	42022613	42022614	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	AP3M2	NM_001134296	exon6	c.608_609insG	p.Q203fs	.	.	310.0	140.0	299.0	0.0	.	41	.	.	Atlas-Indel,Pindel
IYD	389434	hgsc.bcm.edu	hg19	6	150713484	150713493	+	Frame_Shift_Del	DEL	CAGCCCCGAG	CAGCCCCGAG	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	CAGCCCCGAG	CAGCCCCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	IYD	NM_203395	exon3	c.373_382del	p.125_128del	.	.	46.0	12.0	65.0	0.0	.	106	.	.	Atlas-Indel,Pindel
ZNF835	90485	hgsc.bcm.edu	hg19	19	57176266	57176266	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ZNF835	NM_001005850	exon2	c.302delA	p.E101fs	.	.	80.0	38.0	81.0	0.0	.	106	.	.	Atlas-Indel,Pindel
C1orf170	84808	hgsc.bcm.edu	hg19	1	915475	915476	+	RNA	INS	-	-	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	C1orf170	.	.	.	.	.	.	237.0	23.0	212.0	0.0	.	5	.	.	Atlas-INDEL
SPINK5	11005	hgsc.bcm.edu	hg19	5	147503432	147503432	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SPINK5	NM_001127699	exon27	c.2574delT	p.N858fs	.	.	170.0	93.0	189.0	0.0	.	245	.	.	Atlas-Indel,Pindel
NHS	4810	hgsc.bcm.edu	hg19	X	17710579	17710579	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NHS	NM_198270	exon3	c.842delA	p.H281fs	.	.	191.0	88.0	267.0	0.0	.	302	.	.	Atlas-Indel,Pindel
IFNL1	282618	hgsc.bcm.edu	hg19	19	39787118	39787119	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	.	NM_172140	exon1	c.57_58insG	p.A19fs	.	.	111.0	10.0	124.0	0.0	.	.	.	.	Atlas-INDEL
OBSL1	23363	hgsc.bcm.edu	hg19	2	220432912	220432913	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	OBSL1	NM_001173431	exon2	c.1147_1148insC	p.C383fs	.	.	163.0	10.0	148.0	0.0	.	120	.	.	Atlas-INDEL
ABHD16A	7920	hgsc.bcm.edu	hg19	6	31657365	31657366	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ABHD16A	NM_021160	exon12	c.1074_1075insG	p.G358fs	.	.	97.0	10.0	57.0	0.0	.	34	.	.	Atlas-INDEL
ANKH	56172	hgsc.bcm.edu	hg19	5	14716830	14716832	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ANKH	NM_054027	exon9	c.1125_1127del	p.375_376del	.	.	149.0	41.0	137.0	0.0	.	64	.	.	Atlas-Indel,Pindel
SPIRE1	56907	hgsc.bcm.edu	hg19	18	12453128	12453128	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SPIRE1	NM_001128626	exon14	c.1787delG	p.C596fs	.	.	225.0	22.0	281.0	0.0	.	120	.	.	Atlas-Indel,Pindel
MUC16	94025	hgsc.bcm.edu	hg19	19	9045850	9045853	+	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	MUC16	NM_024690	exon5	c.35779_35782del	p.11927_11928del	.	.	236.0	89.0	317.0	0.0	.	4315	.	.	Atlas-Indel,Pindel
RGPD4	285190	hgsc.bcm.edu	hg19	2	108487515	108487515	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	RGPD4	NM_182588	exon20	c.3054delC	p.S1018fs	.	.	311.0	121.0	398.0	0.0	.	112	.	.	Atlas-INDEL
CD7	924	hgsc.bcm.edu	hg19	17	80273282	80273283	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CD7	NM_006137	exon4	c.638_639insG	p.D213fs	.	.	87.0	10.0	73.0	0.0	.	25	.	.	Atlas-INDEL
APOB	338	hgsc.bcm.edu	hg19	2	21228142	21228157	+	Frame_Shift_Del	DEL	GGAGGGAATCTCAATG	GGAGGGAATCTCAATG	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	GGAGGGAATCTCAATG	GGAGGGAATCTCAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	APOB	NM_000384	exon26	c.11584_11599del	p.3862_3867del	.	.	145.0	33.0	242.0	0.0	.	761	.	.	Atlas-Indel,Pindel
SALL2	6297	hgsc.bcm.edu	hg19	14	21991412	21991413	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	SALL2	NM_005407	exon2	c.2450_2451insG	p.A817fs	.	.	162.0	10.0	178.0	0.0	.	95	.	.	Atlas-INDEL
TIAL1	7073	hgsc.bcm.edu	hg19	10	121337034	121337034	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	TIAL1	NM_001033925	exon9	c.718delC	p.Q240fs	.	.	153.0	65.0	153.0	0.0	.	47	.	.	Atlas-Indel,Pindel
CHD9	80205	hgsc.bcm.edu	hg19	16	53352155	53352156	+	Frame_Shift_Ins	INS	-	-	AAAAAGAC	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	CHD9	NM_025134	exon37	c.7568_7569insAAAAAGAC	p.Q2523fs	.	.	64.0	25.0	370.0	0.0	.	203	.	.	Atlas-Indel,Pindel
ADAM12	8038	hgsc.bcm.edu	hg19	10	127708372	127708372	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	ADAM12	NM_003474	exon22	c.2562delT	p.P854fs	.	.	91.0	37.0	105.0	0.0	.	388	.	.	Atlas-Indel,Pindel
NLGN1	22871	hgsc.bcm.edu	hg19	3	173993239	173993240	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NLGN1	NM_014932	exon5	c.780_781del	p.260_261del	.	.	322.0	62.0	266.0	0.0	.	209	.	.	Pindel
NCOR1	9611	hgsc.bcm.edu	hg19	17	15973503	15973503	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	.	NCOR1	NM_001190440	exon30	c.4538delC	p.P1513fs	.	.	86.0	43.0	160.0	0.0	.	240	.	.	Pindel
ALK	238	hgsc.bcm.edu	hg19	2	29443612	29443612	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10Z-01A-11D-A12Z-10	TCGA-BC-A10Z-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	e6bbfd9b-d3b5-4611-9011-ec67b57f3577	40a34014-00b9-4b89-9e56-3e2e6bc78a52	ALK,NS,carcinoma,0,1	ALK	NM_004304	exon23	c.3606delA	p.G1202fs	.	.	118.0	29.0	90.0	0.0	.	533	.	.	Pindel