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
VWA5B1	127731	hgsc.bcm.edu	hg19	1	20657389	20657389	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	VWA5B1	NM_001039500	exon11	c.C1485A	p.N495K	ACCCAACGTCTGC	.	145.0	81.0	204.0	0.0	.	44	.	.	Atlas-SNP
DNAJC6	9829	hgsc.bcm.edu	hg19	1	65775451	65775451	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DNAJC6	NM_001256864	exon1	c.G23A	p.R8Q	GCTACCGGAAAAA	.	120.0	29.0	146.0	0.0	.	104	.	.	Atlas-SNP
SLC44A5	204962	hgsc.bcm.edu	hg19	1	75805298	75805298	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SLC44A5	NM_152697	exon4	c.G70T	p.D24Y	CTGGGTCATATGT	.	65.0	14.0	74.0	0.0	.	231	.	.	Atlas-SNP
KCNC4	3749	hgsc.bcm.edu	hg19	1	110775555	110775555	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	KCNC4_ENST00000438661,NS,carcinoma,0,1	KCNC4	NM_001039574	exon4	c.G1842A	p.S614S	CCTCTCGTCCAAC	.	37.0	25.0	69.0	0.0	.	113	.	.	Atlas-SNP
PLEKHO1	51177	hgsc.bcm.edu	hg19	1	150131276	150131276	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PLEKHO1	NM_016274	exon6	c.C788T	p.P263L	TGACGCCCACAGA	.	303.0	15.0	117.0	0.0	.	37	.	.	Atlas-SNP
PLEKHO1	51177	hgsc.bcm.edu	hg19	1	150131673	150131673	+	Silent	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	PLEKHO1,bladder,carcinoma,0,1	PLEKHO1	NM_016274	exon6	c.C1185G	p.L395L	CCACCTCAGACAG	.	390.0	16.0	165.0	0.0	.	37	.	.	Atlas-SNP
DHX9	1660	hgsc.bcm.edu	hg19	1	182823304	182823304	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DHX9	NM_001357	exon6	c.A617G	p.D206G	GTCCTGATCACAA	.	166.0	100.0	223.0	0.0	.	114	.	.	Atlas-SNP
TRIM54	57159	hgsc.bcm.edu	hg19	2	27528584	27528584	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TRIM54	NM_032546	exon6	c.G868C	p.G290R	GTCCGCGGCCTCA	.	79.0	33.0	100.0	0.0	.	35	.	.	Atlas-SNP
LOC728819	0	hgsc.bcm.edu	hg19	2	43903342	43903342	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	.	NM_001101330	exon1	c.C120T	p.H40H	GTGCTCGTGGTCT	.	377.0	173.0	448.0	0.0	.	.	.	.	Atlas-SNP
TCF7L1	83439	hgsc.bcm.edu	hg19	2	85361140	85361140	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TCF7L1	NM_031283	exon2	c.C251A	p.A84E	CGCAGGCGGAGAG	.	41.0	24.0	80.0	0.0	.	44	.	.	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	hg19	2	109381074	109381074	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	RANBP2	NM_006267	exon20	c.G4079A	p.S1360N	GTAACAGCTGCTC	.	112.0	53.0	157.0	0.0	.	488	.	.	Atlas-SNP
KCNJ3	3760	hgsc.bcm.edu	hg19	2	155555841	155555841	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	KCNJ3	NM_001260509	exon1	c.C554A	p.S185Y	AGATGTCCCAGCC	.	79.0	17.0	87.0	0.0	.	126	.	.	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	hg19	2	168100239	168100239	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	XIRP2	NM_152381	exon9	c.G2337T	p.L779F	GCCGTTGGACACA	.	230.0	114.0	305.0	0.0	.	914	.	.	Atlas-SNP
OSBPL6	114880	hgsc.bcm.edu	hg19	2	179170928	179170928	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	OSBPL6	NM_001201482	exon3	c.A17G	p.K6R	ATGAGAAGGGCAT	.	83.0	46.0	110.0	0.0	.	178	.	.	Atlas-SNP
HIBCH	26275	hgsc.bcm.edu	hg19	2	191155206	191155206	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HIBCH	NM_014362	exon5	c.T310G	p.S104A	CTTCCGAGATCAC	.	135.0	58.0	136.0	0.0	.	28	.	.	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	hg19	2	196825086	196825086	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DNAH7	NM_018897	exon18	c.T2789C	p.L930S	GATGCCAAAATAA	.	98.0	44.0	108.0	0.0	.	512	.	.	Atlas-SNP
SGOL2	151246	hgsc.bcm.edu	hg19	2	201400832	201400832	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	SGOL2,bladder,carcinoma,0,1	SGOL2	NM_001160046	exon4	c.G354C	p.L118F	TAACTTGATAACT	.	97.0	40.0	101.0	0.0	.	126	.	.	Atlas-SNP
ABI2	10152	hgsc.bcm.edu	hg19	2	204193320	204193320	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ABI2	NM_005759	exon1	c.G83T	p.R28L	TGGAACGGGTGGC	.	80.0	34.0	104.0	0.0	.	44	.	.	Atlas-SNP
DYTN	391475	hgsc.bcm.edu	hg19	2	207530732	207530732	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DYTN	NM_001093730	exon10	c.C1002A	p.N334K	GTATTGGTTTAAC	.	283.0	131.0	364.0	1.0	.	168	.	.	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	hg19	3	47030821	47030821	+	Silent	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	NBEAL2	NM_015175	exon5	c.C423G	p.L141L	GCTTCTCTGCGAG	.	74.0	29.0	91.0	0.0	.	267	.	.	Atlas-SNP
ROBO2	6092	hgsc.bcm.edu	hg19	3	77629195	77629195	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ROBO2	NM_002942	exon16	c.A2426C	p.Q809P	GTATTCAATACCG	.	98.0	86.0	206.0	0.0	.	527	.	.	Atlas-SNP
KIAA1407	57577	hgsc.bcm.edu	hg19	3	113737618	113737618	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	KIAA1407	NM_020817	exon8	c.T1070A	p.L357Q	ACCTTCAGCTGAA	.	74.0	16.0	86.0	0.0	.	80	.	.	Atlas-SNP
HGD	3081	hgsc.bcm.edu	hg19	3	120365198	120365198	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HGD	NM_000187	exon9	c.A565T	p.S189C	CTATGCTGAACCG	.	41.0	20.0	45.0	0.0	.	65	.	.	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	hg19	3	123411616	123411616	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	MYLK	NM_053025	exon19	c.C3531T	p.G1177G	CGCCTGGCCAGCG	.	48.0	24.0	81.0	0.0	.	224	.	.	Atlas-SNP
SHOX2	6474	hgsc.bcm.edu	hg19	3	157820591	157820591	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SHOX2	NM_003030	exon3	c.G503A	p.R168Q	TTGGTCCGACTTC	.	202.0	95.0	264.0	1.0	.	84	.	.	Atlas-SNP
TMEM175	84286	hgsc.bcm.edu	hg19	4	944240	944240	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TMEM175	NM_032326	exon4	c.C224A	p.A75E	TTCTGGCAACACG	.	111.0	44.0	182.0	0.0	.	44	.	.	Atlas-SNP
TBC1D14	57533	hgsc.bcm.edu	hg19	4	7026792	7026792	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	TBC1D14_ENST00000409757,colon,carcinoma,0,2	TBC1D14	NM_001113361	exon13	c.T1819C	p.F607L	GACGTGTTCTGTC	.	203.0	47.0	276.0	1.0	.	110	.	.	Atlas-SNP
TRMT44	152992	hgsc.bcm.edu	hg19	4	8469838	8469838	+	Silent	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TRMT44	NM_152544	exon9	c.C1692T	p.V564V	CAGGGTCGGGTGT	.	123.0	5.0	155.0	0.0	.	7	.	.	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	hg19	4	30724910	30724910	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PCDH7	NM_032457	exon1	c.C1866A	p.S622R	GGGCAGCACTACG	.	89.0	36.0	68.0	0.0	.	215	.	.	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	hg19	4	30725405	30725405	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PCDH7	NM_032457	exon1	c.T2361A	p.N787K	AGGAAATCCCTTC	.	89.0	38.0	104.0	0.0	.	215	.	.	Atlas-SNP
LPHN3	23284	hgsc.bcm.edu	hg19	4	62936605	62936605	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	LPHN3	NM_015236	exon23	c.T4389C	p.A1463A	ACCGGCTCATTTG	.	86.0	56.0	69.0	0.0	.	800	.	.	Atlas-SNP
NPY5R	4889	hgsc.bcm.edu	hg19	4	164272591	164272591	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	NPY5R	NM_006174	exon4	c.T1166A	p.V389E	TCCATGTGGTAAC	.	154.0	86.0	207.0	0.0	.	101	.	.	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	hg19	4	169201507	169201507	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DDX60	NM_017631	exon14	c.G1957C	p.E653Q	AATGTTCTTTCCA	.	247.0	144.0	307.0	0.0	.	304	.	.	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	hg19	4	169382958	169382958	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DDX60L	NM_001012967	exon5	c.G498A	p.W166X	CATTCCCCAGGAA	.	89.0	30.0	114.0	0.0	.	116	.	.	Atlas-SNP
IRX1	79192	hgsc.bcm.edu	hg19	5	3599577	3599577	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	IRX1	NM_024337	exon2	c.C515A	p.T172K	CCCTCACGCAGGT	.	227.0	116.0	236.0	0.0	.	106	.	.	Atlas-SNP
CTNND2	1501	hgsc.bcm.edu	hg19	5	10992757	10992757	+	Silent	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CTNND2	NM_001332	exon19	c.G3117T	p.S1039S	TGAAGACGAGGCT	.	123.0	60.0	159.0	0.0	.	289	.	.	Atlas-SNP
FSTL4	23105	hgsc.bcm.edu	hg19	5	132534838	132534838	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	FSTL4	NM_015082	exon16	c.G2478C	p.E826D	TGACACCTCACAC	.	66.0	25.0	86.0	0.0	.	74	.	.	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	hg19	5	140209550	140209550	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PCDHA6	NM_018909	exon1	c.G1874A	p.G625E	GCGTGGGGCTGTA	.	118.0	49.0	131.0	0.0	.	442	.	.	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	hg19	5	140347607	140347607	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PCDHAC2	NM_031883	exon1	c.A1256G	p.Y419C	ACTCCTATACACT	.	92.0	49.0	61.0	0.0	.	142	.	.	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	hg19	5	140554546	140554546	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PCDHB7	NM_018940	exon1	c.G2130A	p.R710R	GGTGCGGCTGTGC	.	177.0	28.0	198.0	0.0	.	231	.	.	Atlas-SNP
GPR151	134391	hgsc.bcm.edu	hg19	5	145895523	145895523	+	Missense_Mutation	SNP	C	C	T	rs181265546	bycluster;by1000genomes;alternate_allele	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	GPR151	NM_194251	exon1	c.G154A	p.V52M	TTCCCACGAAGCC	.	105.0	17.0	134.0	0.0	.	35	.	C|1.000;G|0.000	Atlas-SNP
CLK4	57396	hgsc.bcm.edu	hg19	5	178040784	178040784	+	Silent	SNP	A	A	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CLK4	NM_020666	exon6	c.T603A	p.A201A	TGAACGAGCTGCT	.	173.0	65.0	231.0	0.0	.	103	.	.	Atlas-SNP
HIST1H3F	8968	hgsc.bcm.edu	hg19	6	26250628	26250628	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HIST1H3F	NM_021018	exon1	c.A206G	p.Q69R	AGACGCTGGAATG	.	194.0	104.0	191.0	1.0	.	16	.	.	Atlas-SNP
HSPA1L	3305	hgsc.bcm.edu	hg19	6	31777908	31777908	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HSPA1L	NM_005527	exon2	c.A1842G	p.Q614Q	TCCTCCTTGGTAG	.	413.0	120.0	217.0	0.0	.	185	.	.	Atlas-SNP
CPNE5	57699	hgsc.bcm.edu	hg19	6	36712088	36712088	+	Silent	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CPNE5	NM_020939	exon19	c.C1446A	p.P482P	GGACATGGGGAGC	.	80.0	40.0	119.0	0.0	.	56	.	.	Atlas-SNP
DST	667	hgsc.bcm.edu	hg19	6	56480865	56480865	+	Missense_Mutation	SNP	C	C	T	rs200851382		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DST	NM_001723	exon24	c.G7400A	p.R2467H	TTTCTACGGGAGG	.	122.0	30.0	112.0	0.0	.	1427	.	C|0.999;T|0.001	Atlas-SNP
RIMS1	22999	hgsc.bcm.edu	hg19	6	72968729	72968729	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	RIMS1	NM_014989	exon18	c.C2968A	p.P990T	CGTTCTCCAACCA	.	104.0	41.0	98.0	0.0	.	278	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152583243	152583243	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SYNE1	NM_182961	exon101	c.G18896T	p.W6299L	CTTTCCCATTTCA	.	212.0	49.0	238.0	0.0	.	3227	.	.	Atlas-SNP
HGF	3082	hgsc.bcm.edu	hg19	7	81339555	81339555	+	Silent	SNP	G	G	T	rs375872396	alternate_allele	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HGF	NM_000601	exon13	c.C1449A	p.P483P	TATTACGGGATCT	.	126.0	58.0	197.0	0.0	.	171	.	.	Atlas-SNP
HGF	3082	hgsc.bcm.edu	hg19	7	81339556	81339556	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HGF	NM_000601	exon13	c.C1448A	p.P483H	ATTACGGGATCTG	.	124.0	59.0	194.0	0.0	.	171	.	.	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	hg19	7	131912231	131912231	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PLXNA4	NM_020911	exon7	c.C1861T	p.P621S	TCCGGGGCACCTC	.	46.0	21.0	115.0	0.0	.	873	.	.	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	hg19	8	10467732	10467732	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	RP1L1	NM_178857	exon4	c.A3876T	p.L1292F	TTCAGCTAACTGC	.	49.0	26.0	132.0	0.0	.	453	.	.	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	hg19	8	77618337	77618337	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	ZFHX4,NS,carcinoma,0,1	ZFHX4	NM_024721	exon2	c.G2014A	p.G672S	CCGGGTGGCTCTT	.	52.0	8.0	96.0	0.0	.	878	.	.	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	hg19	8	130777987	130777987	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	GSDMC	NM_031415	exon4	c.G457C	p.D153H	GGTTGTCCCCTCT	.	53.0	18.0	110.0	0.0	.	71	.	.	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	hg19	9	79824389	79824389	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	VPS13A	NM_001018038	exon6	c.C436T	p.Q146X	GTTACACAGATCA	.	233.0	127.0	332.0	0.0	.	735	.	.	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	hg19	9	104449365	104449365	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	GRIN3A	NM_133445	exon2	c.G817T	p.D273Y	TCCAGTCTTCCTG	.	212.0	77.0	258.0	0.0	.	186	.	.	Atlas-SNP
ADAMTSL2	9719	hgsc.bcm.edu	hg19	9	136402628	136402628	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ADAMTSL2	NM_014694	exon3	c.G192A	p.G64G	TTGCGGGGGTGGG	.	60.0	25.0	115.0	0.0	.	40	.	.	Atlas-SNP
AKR1C1	1645	hgsc.bcm.edu	hg19	10	5009199	5009199	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	AKR1C1	NM_001353	exon3	c.T333C	p.V111V	TTATGTTGACCTC	.	311.0	137.0	347.0	0.0	.	39	.	.	Atlas-SNP
ARMC3	219681	hgsc.bcm.edu	hg19	10	23297251	23297251	+	Silent	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ARMC3	NM_173081	exon15	c.C1876A	p.R626R	TATGGACGAAGTA	.	138.0	21.0	151.0	0.0	.	102	.	.	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	hg19	10	26462898	26462898	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	MYO3A	NM_017433	exon30	c.T3705C	p.A1235A	GGAAGCTATGATC	.	136.0	61.0	156.0	0.0	.	371	.	.	Atlas-SNP
WAPAL	23063	hgsc.bcm.edu	hg19	10	88206050	88206050	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	WAPAL	NM_015045	exon16	c.G3271A	p.E1091K	TCTCTTCTGTACC	.	180.0	104.0	261.0	0.0	.	81	.	.	Atlas-SNP
IDE	3416	hgsc.bcm.edu	hg19	10	94225544	94225544	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	IDE	NM_004969	exon20	c.A2377G	p.I793V	AGTATATCTCGAT	.	186.0	53.0	282.0	0.0	.	77	.	.	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	hg19	11	47436693	47436693	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SLC39A13	NM_001128225	exon9	c.G1023T	p.L341F	CCTCTTGGAAGAA	.	127.0	48.0	136.0	0.0	.	18	.	.	Atlas-SNP
ARHGEF12	23365	hgsc.bcm.edu	hg19	11	120317715	120317715	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ARHGEF12	NM_015313	exon18	c.G1510C	p.E504Q	GATGCAGAGCGAG	.	143.0	42.0	217.0	0.0	.	133	.	.	Atlas-SNP
RECQL	5965	hgsc.bcm.edu	hg19	12	21643210	21643210	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	RECQL	NM_032941	exon5	c.G317C	p.G106A	TCCTTTCCAGCCA	.	94.0	88.0	175.0	0.0	.	45	.	.	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	hg19	12	41967431	41967431	+	Silent	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PDZRN4	NM_001164595	exon10	c.G2850T	p.L950L	GCACCTGGTTAGG	.	60.0	14.0	91.0	0.0	.	346	.	.	Atlas-SNP
HOXC4	3221	hgsc.bcm.edu	hg19	12	54447739	54447739	+	Missense_Mutation	SNP	C	C	A	rs377491433	alternate_allele	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HOXC4	NM_014620	exon3	c.C33A	p.N11K	CTCTAACTACATC	.	87.0	20.0	112.0	0.0	.	29	.	.	Atlas-SNP
WIF1	11197	hgsc.bcm.edu	hg19	12	65448938	65448938	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	WIF1	NM_007191	exon9	c.C978G	p.C326W	ACATTGGCATTTG	.	95.0	24.0	149.0	0.0	.	96	.	.	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	hg19	13	39357273	39357273	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	FREM2	NM_207361	exon5	c.C5708T	p.P1903L	TCATTCCCATCAG	.	182.0	120.0	189.0	0.0	.	385	.	.	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	hg19	14	64518635	64518635	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SYNE2	NM_182914	exon48	c.G8004T	p.L2668F	TGCCTTGACCACT	.	252.0	126.0	291.0	0.0	.	577	.	.	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	hg19	15	41865515	41865515	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TYRO3	NM_006293	exon17	c.G1995A	p.E665E	GGCAGAGGACATG	.	62.0	12.0	115.0	0.0	.	169	.	.	Atlas-SNP
SHC4	399694	hgsc.bcm.edu	hg19	15	49148299	49148299	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SHC4	NM_203349	exon8	c.C1093T	p.H365Y	CGGCATGGCTATC	.	123.0	37.0	163.0	0.0	.	70	.	.	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	hg19	15	94901825	94901825	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	MCTP2	NM_001159643	exon9	c.G1285C	p.E429Q	AAGCATGAGGAAC	.	176.0	95.0	182.0	0.0	.	122	.	.	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	hg19	16	845334	845334	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CHTF18	NM_022092	exon16	c.C2153A	p.T718N	GGATCACCTTCCC	.	52.0	27.0	48.0	0.0	.	52	.	.	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	hg19	16	1551758	1551758	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TELO2	NM_016111	exon11	c.G1456C	p.D486H	GGCTCTGACTCGG	.	37.0	12.0	49.0	0.0	.	44	.	.	Atlas-SNP
ITGAX	3687	hgsc.bcm.edu	hg19	16	31372494	31372494	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ITGAX	NM_000887	exon9	c.T972C	p.D324D	GAAAGATATTCAA	.	96.0	65.0	128.0	0.0	.	198	.	.	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	hg19	17	11775087	11775087	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DNAH9	NM_001372	exon52	c.A10226T	p.Y3409F	GGCCCTACCTGAG	.	77.0	66.0	154.0	0.0	.	695	.	.	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	hg19	17	33749277	33749277	+	Silent	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SLFN12	NM_018042	exon2	c.C771A	p.L257L	GTCATCGAGGTCA	.	167.0	60.0	122.0	0.0	.	56	.	.	Atlas-SNP
NBR1	4077	hgsc.bcm.edu	hg19	17	41345518	41345518	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	NBR1	NM_031862	exon12	c.C1387T	p.H463Y	CTTTCTCACAAAG	.	227.0	32.0	181.0	0.0	.	55	.	.	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	hg19	17	48629417	48629417	+	Silent	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SPATA20	NM_022827	exon14	c.G1833A	p.A611A	GAGTGCGTGGCTC	.	248.0	81.0	223.0	0.0	.	59	.	.	Atlas-SNP
LOC100653515	0	hgsc.bcm.edu	hg19	17	76888033	76888033	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	.	NM_001243540	exon3	c.G553T	p.G185C	GCTGGCCCAACTC	.	238.0	144.0	179.0	0.0	.	.	.	.	Atlas-SNP
ANKRD12	23253	hgsc.bcm.edu	hg19	18	9182491	9182491	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ANKRD12	NM_001083625	exon2	c.A61G	p.M21V	AGCAATATGGTAG	.	53.0	35.0	81.0	0.0	.	167	.	.	Atlas-SNP
HRH4	59340	hgsc.bcm.edu	hg19	18	22057509	22057509	+	Silent	SNP	C	C	A	rs115905515	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	HRH4	NM_021624	exon3	c.C1156A	p.R386R	CACAGTCGGTCAG	.	80.0	30.0	83.0	0.0	.	46	.	C|0.998;T|0.002	Atlas-SNP
DSC2	1824	hgsc.bcm.edu	hg19	18	28650707	28650707	+	Silent	SNP	A	A	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DSC2	NM_024422	exon14	c.T2235A	p.P745P	ATCTCCAGGAGCT	.	114.0	73.0	166.0	0.0	.	168	.	.	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	hg19	18	29890226	29890226	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	FAM59A,NS,adenocarcinoma,0,1	.	NM_022751	exon3	c.G323T	p.S108I	TCCACACTGTTGA	.	179.0	50.0	275.0	0.0	.	.	.	.	Atlas-SNP
DTNA	1837	hgsc.bcm.edu	hg19	18	32438291	32438291	+	Silent	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	DTNA	NM_001390	exon15	c.A1494G	p.E498E	GCATGAACAAGCT	.	74.0	42.0	113.0	0.0	.	321	.	.	Atlas-SNP
MALT1	10892	hgsc.bcm.edu	hg19	18	56401614	56401614	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	MALT1	NM_006785	exon12	c.1475+1G>A	.	TGCCACGTAAGAA	.	117.0	73.0	198.0	0.0	.	55	.	.	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	hg19	18	59768329	59768329	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PIGN	NM_176787	exon22	c.A2056G	p.I686V	TAATAATTTGATT	.	56.0	37.0	81.0	0.0	.	62	.	.	Atlas-SNP
ZNF729	100287226	hgsc.bcm.edu	hg19	19	22499233	22499233	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ZNF729	NM_001242680	exon4	c.C3014A	p.S1005X	ATTCCTCAACCCT	.	130.0	61.0	137.0	0.0	.	78	.	.	Atlas-SNP
ZNF229	7772	hgsc.bcm.edu	hg19	19	44934591	44934591	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ZNF229	NM_014518	exon6	c.G365C	p.C122S	ACTCTACAGTCTT	.	106.0	25.0	169.0	0.0	.	123	.	.	Atlas-SNP
SYT3	84258	hgsc.bcm.edu	hg19	19	51133064	51133064	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SYT3	NM_032298	exon3	c.C1039A	p.R347S	TCTTGCGGTCAGG	.	35.0	7.0	91.0	0.0	.	85	.	.	Atlas-SNP
LILRA5	353514	hgsc.bcm.edu	hg19	19	54823336	54823336	+	Silent	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	LILRA5	NM_181879	exon4	c.G207T	p.G69G	CAGGGTCCCCTGA	.	204.0	122.0	297.0	1.0	.	49	.	.	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	hg19	19	55111991	55111991	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	LILRA1	NM_006863	exon9	c.C1327A	p.L443I	AACACCCTCAGCC	.	62.0	15.0	103.0	0.0	.	105	.	.	Atlas-SNP
ERGIC3	51614	hgsc.bcm.edu	hg19	20	34130635	34130635	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ERGIC3	NM_015966	exon4	c.C312A	p.F104L	CCTGTTCAAGCAA	.	140.0	53.0	150.0	0.0	.	41	.	.	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	hg19	20	44686186	44686186	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SLC12A5	NM_001134771	exon26	c.T3362G	p.L1121R	AGCACCTGGACCG	.	174.0	67.0	204.0	0.0	.	181	.	.	Atlas-SNP
BACE2	25825	hgsc.bcm.edu	hg19	21	42622762	42622762	+	Silent	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	BACE2	NM_138992	exon7	c.T1068A	p.P356P	CTTCCCTAAAATC	.	209.0	96.0	218.0	0.0	.	45	.	.	Atlas-SNP
CECR1	51816	hgsc.bcm.edu	hg19	22	17662466	17662466	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CECR1	NM_017424	exon9	c.G1443T	p.K481N	ACTGTACCTGCAG	.	121.0	62.0	164.0	0.0	.	77	.	.	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	hg19	22	31533849	31533849	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	PLA2G3	NM_015715	exon4	c.A913T	p.K305X	GCTGCTTCTGTCG	.	189.0	101.0	304.0	0.0	.	85	.	.	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	hg19	22	35717981	35717981	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	TOM1	NM_001135732	exon3	c.A167G	p.K56R	TAAAGAAGAGAAT	.	71.0	24.0	104.0	0.0	.	43	.	.	Atlas-SNP
ARMCX4	100131755	hgsc.bcm.edu	hg19	X	100747169	100747169	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ARMCX4	NM_001256155	exon2	c.G3593T	p.S1198I	AGACTAGTGAGGG	.	9.0	7.0	3.0	0.0	.	2	.	.	Atlas-SNP
IL1RAPL2	26280	hgsc.bcm.edu	hg19	X	105011223	105011223	+	Silent	SNP	T	T	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	IL1RAPL2	NM_017416	exon11	c.T1630C	p.L544L	AGCAAATTAAATT	.	210.0	109.0	246.0	0.0	.	105	.	.	Atlas-SNP
CUL4B	8450	hgsc.bcm.edu	hg19	X	119669737	119669737	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CUL4B	NM_003588	exon18	c.T2162G	p.L721R	CACTGAAGTTTCC	.	573.0	136.0	574.0	0.0	.	181	.	.	Atlas-SNP
IDH3G	3421	hgsc.bcm.edu	hg19	X	153055245	153055245	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	IDH3G	NM_004135	exon5	c.C268T	p.H90Y	TCACGTGCACCTC	.	38.0	12.0	66.0	0.0	.	36	.	.	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	6718	6718	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	.	ENST00000361624	exon1	c.G815A	p.G272D	ACATAGGTATGGT	.	151.0	9.0	575.0	0.0	.	.	.	.	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	7074	7074	+	Nonsense_Mutation	SNP	G	G	A	rs9633436		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	.	ENST00000361624	exon1	c.G1171A	p.G391X	ATCATAGGAGGCT	.	159.0	90.0	472.0	0.0	.	.	.	.	Atlas-SNP
ND3	0	hgsc.bcm.edu	hg19	MT	10401	10401	+	Missense_Mutation	SNP	G	G	A	rs28358278	bycluster;alternate_allele	TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	.	ENST00000361227	exon1	c.G343A	p.E115K	TGAACCGAATTGG	.	167.0	7.0	623.0	0.0	.	.	.	C|0.839;T|0.161	Atlas-SNP
FOXD4L2	100036519	hgsc.bcm.edu	hg19	9	42718188	42718189	+	In_Frame_Ins	INS	-	-	GAG	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	FOXD4L2	NM_001099279	exon1	c.123_124insGAG	p.D41delinsDE	.	.	390.0	46.0	566.0	0.0	.	4	.	.	Atlas-INDEL
SAA1	6288	hgsc.bcm.edu	hg19	11	18290820	18290820	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SAA1	NM_199161	exon3	c.169delC	p.R57fs	.	.	208.0	60.0	217.0	0.0	.	14	.	.	Atlas-Indel,Pindel
FOXD4L2	100036519	hgsc.bcm.edu	hg19	9	70428763	70428764	+	In_Frame_Ins	INS	-	-	CCT	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	FOXD4L2	NM_001099279	exon1	c.137_138insAGG	p.A46delinsEA	.	.	380.0	38.0	585.0	0.0	.	4	.	.	Atlas-INDEL
ANXA13	312	hgsc.bcm.edu	hg19	8	124701110	124701112	+	Frame_Shift_Del	DEL	CCG	CCG	-	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	ANXA13	NM_001003954	exon10	c.841_841del	p.281_281del	.	.	114.0	16.0	184.0	0.0	.	38	.	.	Atlas-INDEL
SAA2	6289	hgsc.bcm.edu	hg19	11	18267513	18267513	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	SAA2	NM_030754	exon3	c.175delA	p.N59fs	.	.	366.0	60.0	428.0	0.0	.	22	.	.	Atlas-Indel,Pindel
CDH22	64405	hgsc.bcm.edu	hg19	20	44856179	44856179	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A217-01A-11D-A152-10	TCGA-BC-A217-10A-01D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	2bff30d5-be79-4686-8164-7a7d9619d3c0	b12f2a60-b900-4c83-9b9e-d1f6bbd469f9	.	CDH22	NM_021248	exon4	c.639delC	p.G213fs	.	.	54.0	30.0	62.0	0.0	.	112	.	.	Atlas-Indel,Pindel
