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
UBE2J2	118424	hgsc.bcm.edu	hg19	1	1192490	1192490	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	UBE2J2	NM_194315	exon6	c.A344G	p.D115G	TGGAAATCCGTGA	.	48.0	4.0	93.0	0.0	.	25	.	.	Atlas-SNP
PRKCZ	5590	hgsc.bcm.edu	hg19	1	2105426	2105426	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PRKCZ	NM_002744	exon14	c.A1376G	p.D459G	ACCCGGACATGAA	.	100.0	4.0	198.0	0.0	.	84	.	.	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	hg19	1	5934637	5934637	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NPHP4	NM_015102	exon22	c.A3125G	p.H1042R	CGCAGGTGGAACA	.	85.0	7.0	144.0	0.0	.	119	.	.	Atlas-SNP
CHD5	26038	hgsc.bcm.edu	hg19	1	6188597	6188597	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CHD5	NM_015557	exon24	c.C3692T	p.A1231V	CTGGCGGCCAAGT	.	79.0	4.0	153.0	0.0	.	267	.	.	Atlas-SNP
NOL9	79707	hgsc.bcm.edu	hg19	1	6589090	6589090	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NOL9	NM_024654	exon10	c.C1789T	p.L597F	GGGCAAGCAGGAT	.	95.0	4.0	176.0	0.0	.	49	.	.	Atlas-SNP
ENO1	2023	hgsc.bcm.edu	hg19	1	8930511	8930511	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ENO1	NM_001428	exon4	c.G240A	p.K80K	TCCTACCTTGCTA	.	54.0	4.0	85.0	0.0	.	38	.	.	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	hg19	1	12908011	12908011	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	HNRNPCL1	NM_001013631	exon2	c.G132A	p.A44A	GCAGCCCGCAATT	.	301.0	60.0	495.0	0.0	.	68	.	.	Atlas-SNP
CLCNKB	1188	hgsc.bcm.edu	hg19	1	16377074	16377074	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CLCNKB	NM_000085	exon11	c.C1032T	p.A344A	CAGCGCCGGCCGC	.	74.0	4.0	102.0	0.0	.	50	.	.	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	hg19	1	19446726	19446726	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	UBR4	NM_020765	exon69	c.A10258G	p.N3420D	AAGAATTGGACTC	.	62.0	4.0	136.0	0.0	.	415	.	.	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	hg19	1	19518865	19518865	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	UBR4	NM_020765	exon11	c.A1211G	p.Q404R	AAATTCTGATAGT	.	64.0	4.0	114.0	0.0	.	415	.	.	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	hg19	1	21936087	21936087	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RAP1GAP	NM_001145658	exon15	c.A1244G	p.D415G	GCGGGGTCCGGGA	.	88.0	5.0	145.0	0.0	.	119	.	.	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	hg19	1	22191789	22191789	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	HSPG2	NM_005529	exon35	c.A4384G	p.M1462V	GGAACATGATCTC	.	95.0	4.0	165.0	0.0	.	311	.	.	Atlas-SNP
KDM1A	23028	hgsc.bcm.edu	hg19	1	23409728	23409728	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	KDM1A	NM_001009999	exon21	c.A2502G	p.T834T	AGCCACAGTGCAT	.	84.0	5.0	199.0	0.0	.	49	.	.	Atlas-SNP
CNKSR1	10256	hgsc.bcm.edu	hg19	1	26514760	26514760	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CNKSR1	NM_006314	exon17	c.A1490G	p.Y497C	CCAAGTACCAGTC	.	78.0	42.0	118.0	0.0	.	66	.	.	Atlas-SNP
ARID1A	8289	hgsc.bcm.edu	hg19	1	27056354	27056354	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ARID1A	NM_006015	exon2	c.G1350A	p.Q450Q	ACAGCAGGTAGAT	.	223.0	129.0	315.0	1.0	.	842	.	.	Atlas-SNP
SLC9A1	6548	hgsc.bcm.edu	hg19	1	27429041	27429041	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	SLC9A1,NS,carcinoma,0,1	SLC9A1	NM_003047	exon8	c.G1655A	p.R552Q	TTAAACCGGTTGA	.	18.0	2.0	42.0	0.0	.	68	.	.	Atlas-SNP
PTPRU	10076	hgsc.bcm.edu	hg19	1	29641992	29641992	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PTPRU	NM_005704	exon24	c.C3366T	p.S1122S	CTGCTCCCGGCGT	.	82.0	48.0	161.0	0.0	.	374	.	.	Atlas-SNP
NKAIN1	79570	hgsc.bcm.edu	hg19	1	31656794	31656794	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NKAIN1	NM_024522	exon4	c.G341T	p.G114V	AGGCAGCCTGGCC	.	88.0	4.0	112.0	0.0	.	21	.	.	Atlas-SNP
COL16A1	1307	hgsc.bcm.edu	hg19	1	32149600	32149600	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	COL16A1	NM_001856	exon33	c.A2288G	p.Q763R	CCGGGTTGGCCCT	.	105.0	5.0	164.0	0.0	.	137	.	.	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	hg19	1	32280899	32280899	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SPOCD1	NM_144569	exon2	c.A36G	p.T12T	GTCTCCTGTGCTG	.	59.0	4.0	102.0	0.0	.	109	.	.	Atlas-SNP
KPNA6	23633	hgsc.bcm.edu	hg19	1	32631794	32631794	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	KPNA6	NM_012316	exon11	c.T1079C	p.I360T	GGACTATTTCAAA	.	91.0	4.0	142.0	0.0	.	34	.	.	Atlas-SNP
IQCC	55721	hgsc.bcm.edu	hg19	1	32673299	32673299	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	IQCC	NM_001160042	exon5	c.G1257A	p.R419R	GTCCAGGACACAG	.	72.0	4.0	139.0	0.0	.	46	.	.	Atlas-SNP
ZBTB8B	728116	hgsc.bcm.edu	hg19	1	32950745	32950745	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ZBTB8B	NM_001145720	exon4	c.G1214T	p.R405I	GCAGGAGAACATT	.	113.0	5.0	165.0	0.0	.	28	.	.	Atlas-SNP
AK2	204	hgsc.bcm.edu	hg19	1	33478978	33478978	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	AK2	NM_013411	exon6	c.G524A	p.R175Q	TCTGATCGACGGA	.	109.0	44.0	161.0	0.0	.	27	.	.	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	hg19	1	34035040	34035040	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CSMD2	NM_052896	exon53	c.G8071A	p.V2691M	AGCCCACCAGTGT	.	77.0	4.0	98.0	0.0	.	946	.	.	Atlas-SNP
STK40	83931	hgsc.bcm.edu	hg19	1	36814304	36814304	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	STK40	NM_032017	exon8	c.A736G	p.S246G	TACCGCTGAGCAC	.	92.0	4.0	94.0	0.0	.	53	.	.	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	hg19	1	38186511	38186511	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	EPHA10	NM_001099439	exon12	c.A2152G	p.T718A	TCAAGGTGCTTCC	.	84.0	5.0	94.0	0.0	.	120	.	.	Atlas-SNP
MTF1	4520	hgsc.bcm.edu	hg19	1	38281033	38281033	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MTF1	NM_005955	exon11	c.T2037C	p.S679S	GGCTGAAGAGAAA	.	97.0	4.0	126.0	0.0	.	67	.	.	Atlas-SNP
FHL3	2275	hgsc.bcm.edu	hg19	1	38463119	38463119	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FHL3	NM_004468	exon6	c.A801G	p.G267G	TTGGTCTCCATCC	.	76.0	4.0	86.0	0.0	.	9	.	.	Atlas-SNP
SCMH1	22955	hgsc.bcm.edu	hg19	1	41493981	41493981	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SCMH1	NM_001031694	exon16	c.G1868T	p.G623V	GCCTTGCCATCGA	.	94.0	4.0	145.0	0.0	.	120	.	.	Atlas-SNP
BTBD19	149478	hgsc.bcm.edu	hg19	1	45275896	45275896	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	BTBD19	NM_001136537	exon2	c.T98C	p.F33S	TTTGCTTCGTGGT	.	80.0	4.0	65.0	0.0	.	16	.	.	Atlas-SNP
TTC4	7268	hgsc.bcm.edu	hg19	1	55194027	55194027	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TTC4	NM_004623	exon6	c.A603G	p.E201E	AATTGAACAGAGG	.	165.0	7.0	72.0	0.0	.	21	.	.	Atlas-SNP
ST6GALNAC5	81849	hgsc.bcm.edu	hg19	1	77334294	77334294	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ST6GALNAC5	NM_030965	exon2	c.A128G	p.Q43R	AGCAGCAGCAGCA	.	190.0	8.0	62.0	0.0	.	59	.	.	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	hg19	1	103364262	103364262	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	COL11A1	NM_080629	exon56	c.A4244T	p.K1415M	CCAGGCTTTCCTG	.	421.0	63.0	202.0	0.0	.	972	.	.	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	hg19	1	120461034	120461034	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	NOTCH2,colon,carcinoma,0,1	NOTCH2	NM_024408	exon32	c.A5924G	p.D1975G	CCATGGTCATCCA	.	181.0	9.0	100.0	0.0	.	348	.	.	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	hg19	1	120539927	120539927	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NOTCH2	NM_001200001	exon4	c.C444T	p.C148C	AGACAGGCAGGCA	.	614.0	406.0	317.0	1.0	.	348	.	.	Atlas-SNP
LIX1L	128077	hgsc.bcm.edu	hg19	1	145497479	145497479	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LIX1L	NM_153713	exon4	c.G684A	p.L228L	AATGTTGGAGTTC	.	537.0	73.0	205.0	0.0	.	28	.	.	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	hg19	1	145530929	145530929	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	ITGA10,NS,carcinoma,0,1	ITGA10	NM_003637	exon7	c.G661T	p.D221Y	CTGGGAGATTTCC	.	482.0	23.0	175.0	0.0	.	131	.	.	Atlas-SNP
CTSK	1513	hgsc.bcm.edu	hg19	1	150778691	150778691	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CTSK	NM_000396	exon3	c.A130G	p.I44V	GAGAGATTTCATC	.	341.0	258.0	133.0	1.0	.	27	.	.	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	hg19	1	152748869	152748869	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LCE1F	NM_178354	exon1	c.C22A	p.Q8K	AGCCAGCAGCAGT	.	841.0	640.0	260.0	0.0	.	42	.	.	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	hg19	1	156909536	156909536	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ARHGEF11	NM_198236	exon37	c.T3900C	p.G1300G	CCCTTCACCCCCA	.	164.0	7.0	71.0	0.0	.	168	.	.	Atlas-SNP
KLHDC9	126823	hgsc.bcm.edu	hg19	1	161068368	161068368	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	KLHDC9	NM_001007255	exon1	c.T43C	p.W15R	TCAGGCTGGGCCT	.	345.0	17.0	79.0	0.0	.	16	.	.	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	hg19	1	173526509	173526509	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	SLC9A11,NS,carcinoma,0,1	.	NM_178527	exon10	c.C1185T	p.L395L	TTCAGCGAGATTA	.	1002.0	105.0	366.0	1.0	.	.	.	.	Atlas-SNP
PAPPA2	60676	hgsc.bcm.edu	hg19	1	176668293	176668293	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PAPPA2	NM_020318	exon8	c.T2804C	p.V935A	CTGAGGTCCACCT	.	196.0	9.0	68.0	0.0	.	665	.	.	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	hg19	1	186064493	186064493	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	HMCN1	NM_031935	exon68	c.A10413G	p.R3471R	GCTTAGAGATGGC	.	168.0	7.0	78.0	0.0	.	797	.	.	Atlas-SNP
CFH	3075	hgsc.bcm.edu	hg19	1	196705955	196705955	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CFH	NM_000186	exon16	c.G2415T	p.M805I	TTTAGTGGCACAA	.	105.0	6.0	59.0	0.0	.	251	.	.	Atlas-SNP
TMEM206	55248	hgsc.bcm.edu	hg19	1	212558758	212558758	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	TMEM206,NS,carcinoma,0,1	TMEM206	NM_001198862	exon5	c.T536C	p.L179S	GGGTACAAGGCAA	.	74.0	3.0	132.0	0.0	.	41	.	.	Atlas-SNP
PROX1	5629	hgsc.bcm.edu	hg19	1	214171377	214171377	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PROX1	NM_001270616	exon2	c.C1499T	p.P500L	GTGCTCCCTCCGG	.	61.0	4.0	86.0	0.0	.	124	.	.	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	hg19	1	216373309	216373309	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	USH2A	NM_007123	exon17	c.C3471A	p.I1157I	AGGAATGATATAA	.	116.0	5.0	189.0	0.0	.	1168	.	.	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	hg19	1	217947703	217947703	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SPATA17	NM_138796	exon7	c.A547G	p.R183G	CCCTTCAGAAAAG	.	90.0	4.0	94.0	0.0	.	59	.	.	Atlas-SNP
TGFB2	7042	hgsc.bcm.edu	hg19	1	218578636	218578636	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TGFB2	NM_001135599	exon3	c.A556G	p.K186E	AACCCAAAAGCCA	.	61.0	4.0	135.0	0.0	.	102	.	.	Atlas-SNP
ACTA1	58	hgsc.bcm.edu	hg19	1	229568488	229568488	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ACTA1	NM_001100	exon3	c.A269G	p.H90R	AAGGTGTGGTGCC	.	100.0	4.0	132.0	0.0	.	65	.	.	Atlas-SNP
ABCB10	23456	hgsc.bcm.edu	hg19	1	229666086	229666086	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ABCB10	NM_012089	exon8	c.C1505T	p.P502L	CGAGCTGGATAGG	.	90.0	5.0	119.0	0.0	.	71	.	.	Atlas-SNP
PGBD5	79605	hgsc.bcm.edu	hg19	1	230492867	230492867	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PGBD5	NM_001258311	exon2	c.A532G	p.S178G	AGATGCTGGTGGA	.	69.0	4.0	123.0	0.0	.	73	.	.	Atlas-SNP
C1orf198	84886	hgsc.bcm.edu	hg19	1	230979276	230979276	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	C1orf198,NS,carcinoma,0,1	C1orf198	NM_032800	exon3	c.G751T	p.E251X	GCTGCTCCTGACG	.	48.0	2.0	84.0	0.0	.	29	.	.	Atlas-SNP
C1orf198	84886	hgsc.bcm.edu	hg19	1	231004122	231004122	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	C1orf198	NM_032800	exon1	c.A137G	p.D46G	TCCTTGTCCTGCA	.	108.0	5.0	110.0	0.0	.	29	.	.	Atlas-SNP
LYST	1130	hgsc.bcm.edu	hg19	1	235922305	235922305	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LYST	NM_000081	exon23	c.A6848G	p.E2283G	TTTGGCTCATAAC	.	85.0	5.0	126.0	0.0	.	370	.	.	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	hg19	1	240370245	240370245	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FMN2	NM_020066	exon5	c.T2133C	p.L711L	AGGGCTTGAGAAT	.	73.0	4.0	142.0	0.0	.	451	.	.	Atlas-SNP
ZBTB18	10472	hgsc.bcm.edu	hg19	1	244218512	244218512	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	.	NM_205768	exon2	c.G1436A	p.W479X	GCAAGTGGTGCGA	.	76.0	4.0	105.0	0.0	.	.	.	.	Atlas-SNP
TFB2M	64216	hgsc.bcm.edu	hg19	1	246727677	246727677	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TFB2M	NM_022366	exon2	c.A373G	p.S125G	TGTCACTTTCGAG	.	90.0	4.0	128.0	0.0	.	46	.	.	Atlas-SNP
OR6F1	343169	hgsc.bcm.edu	hg19	1	247875175	247875175	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	OR6F1	NM_001005286	exon1	c.A883T	p.K295X	CTTCCTTATTACG	.	84.0	4.0	166.0	0.0	.	88	.	.	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	hg19	2	1652432	1652432	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PXDN	NM_012293	exon17	c.G3120A	p.G1040G	CACCTCCCCCAGG	.	80.0	4.0	96.0	0.0	.	255	.	.	Atlas-SNP
ASAP2	8853	hgsc.bcm.edu	hg19	2	9541497	9541497	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ASAP2	NM_003887	exon27	c.T2918C	p.V973A	TCATCGTGGACGG	.	148.0	7.0	138.0	0.0	.	91	.	.	Atlas-SNP
E2F6	1876	hgsc.bcm.edu	hg19	2	11587894	11587894	+	Missense_Mutation	SNP	T	T	C	rs371114161		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	E2F6	NM_198256	exon6	c.A658G	p.I220V	CTGTGATAGAGTC	.	141.0	55.0	265.0	0.0	.	17	.	.	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	hg19	2	15514800	15514800	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NBAS	NM_015909	exon31	c.A3635G	p.E1212G	AGCTCCTCTTGAA	.	119.0	5.0	100.0	0.0	.	246	.	.	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	hg19	2	15534402	15534402	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NBAS	NM_015909	exon28	c.C3206A	p.S1069X	TCTTCTGAGCTAG	.	130.0	6.0	143.0	0.0	.	246	.	.	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	hg19	2	26693459	26693459	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	OTOF	NM_194248	exon33	c.4023+2T>C	.	GGTCTCACCTCCT	.	97.0	4.0	131.0	0.0	.	524	.	.	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	hg19	2	27803857	27803857	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	C2orf16	NM_032266	exon1	c.A4418G	p.Q1473R	TGGGGCAGCCTCT	.	74.0	5.0	78.0	0.0	.	357	.	.	Atlas-SNP
FOSL2	2355	hgsc.bcm.edu	hg19	2	28627206	28627206	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	FOSL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	FOSL2	NM_005253	exon2	c.G335A	p.R112H	TGGGCCGCAGGAG	.	70.0	3.0	67.0	0.0	.	39	.	.	Atlas-SNP
THADA	63892	hgsc.bcm.edu	hg19	2	43519292	43519292	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	THADA	NM_001083953	exon33	c.A4888G	p.T1630A	TTGGGGTCAGATG	.	104.0	5.0	120.0	0.0	.	131	.	.	Atlas-SNP
FBXO11	80204	hgsc.bcm.edu	hg19	2	48037548	48037548	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FBXO11	NM_001190274	exon19	c.G2245T	p.D749Y	AAATATCATTTTC	.	85.0	4.0	99.0	0.0	.	127	.	.	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	hg19	2	54122147	54122147	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PSME4	NM_014614	exon34	c.A3909G	p.T1303T	TACCTCTGTCATA	.	95.0	4.0	95.0	0.0	.	247	.	.	Atlas-SNP
PUS10	150962	hgsc.bcm.edu	hg19	2	61175283	61175283	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PUS10	NM_144709	exon16	c.T1346C	p.L449P	CGGTGAAGGACGC	.	123.0	5.0	152.0	0.0	.	49	.	.	Atlas-SNP
XPO1	7514	hgsc.bcm.edu	hg19	2	61706090	61706090	+	Silent	SNP	A	A	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	XPO1	NM_003400	exon25	c.T3081G	p.G1027G	GTCTTCACCTGCA	.	189.0	59.0	241.0	0.0	.	108	.	.	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	hg19	2	69053300	69053300	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ARHGAP25	NM_001007231	exon11	c.A1915G	p.M639V	AAATCCATGAAGG	.	67.0	4.0	102.0	0.0	.	175	.	.	Atlas-SNP
ADD2	119	hgsc.bcm.edu	hg19	2	70919547	70919547	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ADD2	NM_001185055	exon6	c.G741A	p.P247P	TGTGGCCGGTGTG	.	92.0	4.0	78.0	0.0	.	261	.	.	Atlas-SNP
LOXL3	84695	hgsc.bcm.edu	hg19	2	74763252	74763252	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LOXL3	NM_032603	exon7	c.A1119G	p.E373E	GCGAACTTCACTC	.	61.0	4.0	73.0	0.0	.	73	.	.	Atlas-SNP
HK2	3099	hgsc.bcm.edu	hg19	2	75113635	75113635	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	HK2	NM_000189	exon15	c.G2054T	p.C685F	ATGCCTGCTACAT	.	129.0	50.0	143.0	0.0	.	85	.	.	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	hg19	2	84949784	84949784	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DNAH6	NM_001370	exon60	c.A9828G	p.E3276E	GGAAGAAGCAGAG	.	97.0	4.0	112.0	0.0	.	194	.	.	Atlas-SNP
CD8A	925	hgsc.bcm.edu	hg19	2	87013062	87013062	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CD8A	NM_001145873	exon9	c.T689C	p.L230P	GCCGAAAGGCTGG	.	107.0	5.0	105.0	0.0	.	28	.	.	Atlas-SNP
NCAPH	23397	hgsc.bcm.edu	hg19	2	97009872	97009872	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NCAPH	NM_015341	exon6	c.A625G	p.K209E	ACAACCAAAAAGG	.	97.0	4.0	101.0	0.0	.	67	.	.	Atlas-SNP
TMEM131	23505	hgsc.bcm.edu	hg19	2	98410005	98410005	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TMEM131	NM_015348	exon30	c.T3398C	p.L1133P	ACCAAAAGAAACA	.	104.0	7.0	107.0	0.0	.	258	.	.	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	hg19	2	98750292	98750292	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	VWA3B	NM_144992	exon7	c.A878G	p.H293R	GATTCCACGCATT	.	78.0	4.0	89.0	0.0	.	138	.	.	Atlas-SNP
AFF3	3899	hgsc.bcm.edu	hg19	2	100343586	100343586	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	AFF3	NM_001025108	exon10	c.A1119G	p.K373K	ATCACCTTTCTCT	.	80.0	4.0	83.0	0.0	.	164	.	.	Atlas-SNP
TGFBRAP1	9392	hgsc.bcm.edu	hg19	2	105885829	105885829	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TGFBRAP1	NM_004257	exon11	c.T2306C	p.F769S	ATCAGGAATGGGC	.	119.0	5.0	123.0	0.0	.	70	.	.	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	hg19	2	107459744	107459744	+	Silent	SNP	G	G	A	rs144265287	alternate_allele	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ST6GAL2	NM_032528	exon2	c.C690T	p.T230T	GTTGGCGGTCAGG	.	51.0	4.0	31.0	0.0	.	159	.	G|1.000;C|0.000	Atlas-SNP
NPHP1	4867	hgsc.bcm.edu	hg19	2	110881571	110881571	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NPHP1	NM_000272	exon20	c.T1999C	p.S667P	GTGTGGAGTGGAG	.	66.0	4.0	105.0	0.0	.	68	.	.	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	hg19	2	113958938	113958938	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PSD4	NM_012455	exon17	c.A3117G	p.S1039S	CATCTCAGAGCGC	.	69.0	4.0	70.0	0.0	.	74	.	.	Atlas-SNP
CLASP1	23332	hgsc.bcm.edu	hg19	2	122227423	122227423	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CLASP1	NM_001207051	exon9	c.C826T	p.R276C	GCCGGCGGGTGGT	.	108.0	6.0	96.0	0.0	.	135	.	.	Atlas-SNP
CNTNAP5	129684	hgsc.bcm.edu	hg19	2	125204453	125204453	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CNTNAP5	NM_130773	exon6	c.A857G	p.D286G	CGGTGGACAAGCA	.	149.0	6.0	182.0	0.0	.	405	.	.	Atlas-SNP
CYP27C1	339761	hgsc.bcm.edu	hg19	2	127958787	127958787	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CYP27C1	NM_001001665	exon3	c.A299C	p.Y100S	CCTGCATACATGG	.	88.0	31.0	94.0	0.0	.	52	.	.	Atlas-SNP
PROC	5624	hgsc.bcm.edu	hg19	2	128186428	128186428	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PROC	NM_000312	exon9	c.A1292G	p.N431S	TTCACAACTACGG	.	73.0	4.0	63.0	0.0	.	31	.	.	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	hg19	2	128338357	128338357	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MYO7B	NM_001080527	exon10	c.T1040C	p.M347T	ACGTGATGGAGAC	.	83.0	4.0	93.0	0.0	.	359	.	.	Atlas-SNP
GPR148	344561	hgsc.bcm.edu	hg19	2	131487061	131487061	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GPR148	NM_207364	exon1	c.G337A	p.G113S	CTGGGTGGCTGGG	.	140.0	7.0	166.0	0.0	.	54	.	.	Atlas-SNP
R3HDM1	23518	hgsc.bcm.edu	hg19	2	136481779	136481779	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	R3HDM1	NM_015361	exon26	c.A3217G	p.I1073V	AAACAAATTAACT	.	87.0	4.0	124.0	0.0	.	84	.	.	Atlas-SNP
CXCR4	7852	hgsc.bcm.edu	hg19	2	136872711	136872711	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CXCR4	NM_001008540	exon1	c.T799C	p.S267P	TGAAGGAGTCGAT	.	80.0	4.0	109.0	0.0	.	51	.	.	Atlas-SNP
FIGN	55137	hgsc.bcm.edu	hg19	2	164466794	164466794	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FIGN	NM_018086	exon3	c.G1548T	p.T516T	TAAGGCCGTCAGT	.	148.0	55.0	175.0	0.0	.	106	.	.	Atlas-SNP
COBLL1	22837	hgsc.bcm.edu	hg19	2	165552127	165552127	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	COBLL1	NM_014900	exon12	c.A1889G	p.N630S	GGTTGATTCAGTT	.	654.0	232.0	668.0	0.0	.	122	.	.	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	hg19	2	170031784	170031784	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LRP2	NM_004525	exon55	c.G10687A	p.G3563S	AGTTGCCGTCACT	.	200.0	88.0	213.0	0.0	.	751	.	.	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	hg19	2	171323061	171323061	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MYO3B	NM_001083615	exon25	c.C2854T	p.H952Y	CAGCCCCACTTTG	.	75.0	4.0	71.0	0.0	.	320	.	.	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	hg19	2	171710458	171710458	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GAD1	NM_000817	exon14	c.G1339A	p.D447N	TCCTACGACACCG	.	99.0	5.0	134.0	0.0	.	79	.	.	Atlas-SNP
OLA1	29789	hgsc.bcm.edu	hg19	2	174945976	174945976	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	OLA1	NM_013341	exon9	c.T870C	p.S290S	CAAAGCACTGAAA	.	112.0	5.0	97.0	0.0	.	37	.	.	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	hg19	2	196750867	196750867	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DNAH7	NM_018897	exon34	c.G5536A	p.E1846K	TTACCTCAAGCAA	.	88.0	4.0	100.0	0.0	.	512	.	.	Atlas-SNP
CCDC150	284992	hgsc.bcm.edu	hg19	2	197521794	197521794	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CCDC150	NM_001080539	exon4	c.A510G	p.E170E	AGAGGAAGAAGAC	.	98.0	4.0	148.0	0.0	.	96	.	.	Atlas-SNP
GTF3C3	9330	hgsc.bcm.edu	hg19	2	197664292	197664292	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GTF3C3	NM_001206774	exon1	c.A44G	p.K15R	GAGATTTTCCCTT	.	94.0	4.0	102.0	0.0	.	96	.	.	Atlas-SNP
CASP8	841	hgsc.bcm.edu	hg19	2	202134252	202134252	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CASP8	NM_001228	exon4	c.A325G	p.S109G	CGCATGAGCTGGG	.	98.0	6.0	98.0	0.0	.	272	.	.	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	hg19	2	207041288	207041288	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	GPR1,NS,carcinoma,0,1	GPR1	NM_001098199	exon3	c.T684C	p.C228C	GATGAGACACAAG	.	75.0	3.0	102.0	0.0	.	38	.	.	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	hg19	2	209217489	209217489	+	Missense_Mutation	SNP	G	G	T	rs191717036	bycluster;by1000genomes;alternate_allele	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PIKFYVE	NM_015040	exon39	c.G5827T	p.G1943W	TTCTACGGGAGAA	.	53.0	15.0	67.0	0.0	.	223	.	G|1.000;A|0.000	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	hg19	2	209217490	209217490	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PIKFYVE	NM_015040	exon39	c.G5828C	p.G1943A	TCTACGGGAGAAA	.	54.0	15.0	67.0	0.0	.	223	.	.	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	hg19	2	210558811	210558811	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MAP2	NM_002374	exon7	c.T1917C	p.T639T	CAGCACTCTCGCA	.	94.0	4.0	114.0	0.0	.	372	.	.	Atlas-SNP
MAP2	4133	hgsc.bcm.edu	hg19	2	210570348	210570348	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	MAP2_ENST00000199940,caecum,carcinoma,0,3	MAP2	NM_002374	exon11	c.A4629G	p.R1543R	CCCAAGACCTTCC	.	91.0	5.0	105.0	0.0	.	372	.	.	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	hg19	2	211523405	211523405	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CPS1	NM_001122633	exon32	c.A3767G	p.D1256G	GAAATGATGTCTT	.	91.0	4.0	121.0	0.0	.	485	.	.	Atlas-SNP
PECR	55825	hgsc.bcm.edu	hg19	2	216904018	216904018	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PECR	NM_018441	exon8	c.A892G	p.K298E	TCTCCTTAAAGGT	.	100.0	4.0	89.0	0.0	.	22	.	.	Atlas-SNP
RESP18	389075	hgsc.bcm.edu	hg19	2	220194423	220194423	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RESP18	NM_001007089	exon4	c.G401T	p.R134I	TGCAGTCTGCTGG	.	145.0	44.0	150.0	0.0	.	13	.	.	Atlas-SNP
SLC4A3	6508	hgsc.bcm.edu	hg19	2	220506390	220506390	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SLC4A3	NM_201574	exon23	c.T3720C	p.A1240A	AGATGCTGAACCA	.	115.0	5.0	129.0	0.0	.	144	.	.	Atlas-SNP
WDFY1	57590	hgsc.bcm.edu	hg19	2	224746759	224746759	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	WDFY1	NM_020830	exon10	c.T964C	p.C322R	TCCCGCAGACAGC	.	72.0	4.0	58.0	0.0	.	46	.	.	Atlas-SNP
GPR55	9290	hgsc.bcm.edu	hg19	2	231775064	231775064	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GPR55	NM_005683	exon2	c.T614C	p.I205T	ATGTGGATGCTCC	.	92.0	5.0	96.0	0.0	.	46	.	.	Atlas-SNP
NMUR1	10316	hgsc.bcm.edu	hg19	2	232392897	232392897	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NMUR1	NM_006056	exon2	c.T835C	p.S279P	ATCTGGACCTGGC	.	74.0	5.0	86.0	0.0	.	46	.	.	Atlas-SNP
C2orf57	165100	hgsc.bcm.edu	hg19	2	232458839	232458839	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	C2orf57	NM_152614	exon1	c.A1177G	p.N393D	GACCCCAACTATG	.	100.0	4.0	84.0	0.0	.	35	.	.	Atlas-SNP
ECEL1	9427	hgsc.bcm.edu	hg19	2	233344956	233344956	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ECEL1	NM_004826	exon18	c.G2235T	p.L745L	ACTGCCCAGCACC	.	102.0	49.0	143.0	0.0	.	73	.	.	Atlas-SNP
NEU2	4759	hgsc.bcm.edu	hg19	2	233898881	233898881	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NEU2	NM_005383	exon2	c.A257G	p.N86S	CCATGAACCCATG	.	107.0	5.0	119.0	0.0	.	42	.	.	Atlas-SNP
HJURP	55355	hgsc.bcm.edu	hg19	2	234756078	234756078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	HJURP	NM_018410	exon5	c.T367C	p.S123P	GGTCTGACGTGGC	.	134.0	6.0	164.0	0.0	.	72	.	.	Atlas-SNP
BHLHE40	8553	hgsc.bcm.edu	hg19	3	5025019	5025019	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	BHLHE40	NM_003670	exon5	c.T881C	p.L294P	TGCAGCTTTCGGA	.	83.0	5.0	95.0	0.0	.	35	.	.	Atlas-SNP
SETD5	55209	hgsc.bcm.edu	hg19	3	9517690	9517690	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SETD5	NM_001080517	exon23	c.C4244G	p.P1415R	ACTACCCACACCG	.	92.0	4.0	123.0	0.0	.	210	.	.	Atlas-SNP
IL17RE	132014	hgsc.bcm.edu	hg19	3	9944675	9944675	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	IL17RE	NM_153483	exon2	c.T179C	p.L60P	TCGACCTCTCTGA	.	160.0	7.0	136.0	0.0	.	62	.	.	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	hg19	3	14724660	14724660	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	C3orf20	NM_032137	exon3	c.A440G	p.E147G	TGACGGAGCTCCT	.	118.0	5.0	109.0	0.0	.	109	.	.	Atlas-SNP
FGD5	152273	hgsc.bcm.edu	hg19	3	14862587	14862587	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FGD5	NM_152536	exon1	c.A2009G	p.H670R	AATTGCATGTGGA	.	123.0	5.0	148.0	0.0	.	248	.	.	Atlas-SNP
CNOT10	25904	hgsc.bcm.edu	hg19	3	32811404	32811404	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CNOT10	NM_001256742	exon18	c.A2210G	p.E737G	CTAAAGAGGTGCC	.	82.0	4.0	93.0	0.0	.	57	.	.	Atlas-SNP
TRANK1	9881	hgsc.bcm.edu	hg19	3	36874860	36874860	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TRANK1	NM_014831	exon21	c.C6082G	p.Q2028E	CACACTGGCTGGC	.	99.0	4.0	87.0	0.0	.	398	.	.	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	hg19	3	37053518	37053518	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MLH1	NM_000249	exon8	c.C605G	p.A202G	CAGTAGCTGATGT	.	178.0	56.0	209.0	0.0	.	226	.	.	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	hg19	3	38049787	38049787	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PLCD1	NM_001130964	exon13	c.G2037T	p.V679V	GATCTCCACTGTC	.	79.0	4.0	133.0	0.0	.	87	.	.	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	hg19	3	38640487	38640487	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SCN5A	NM_001160160	exon13	c.T1945C	p.C649R	CTACACACGGAGC	.	84.0	4.0	78.0	0.0	.	634	.	.	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	hg19	3	38812863	38812863	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SCN10A	NM_006514	exon4	c.T506C	p.L169S	TTTATCAAGGCTT	.	90.0	5.0	103.0	0.0	.	359	.	.	Atlas-SNP
USP19	10869	hgsc.bcm.edu	hg19	3	49149789	49149789	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	USP19	NM_001199161	exon19	c.A2693G	p.Q898R	TTCCGCTGGCAGG	.	119.0	5.0	109.0	0.0	.	158	.	.	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	hg19	3	49169091	49169091	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LAMB2	NM_002292	exon5	c.C525T	p.Y175Y	ATATCGGTACACA	.	92.0	5.0	68.0	0.0	.	156	.	.	Atlas-SNP
IP6K1	9807	hgsc.bcm.edu	hg19	3	49775655	49775655	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	IP6K1	NM_153273	exon3	c.A424G	p.T142A	CAGAGGTCTCAAG	.	120.0	5.0	118.0	0.0	.	41	.	.	Atlas-SNP
RASSF1	11186	hgsc.bcm.edu	hg19	3	50368106	50368106	+	Missense_Mutation	SNP	C	C	G	rs142957899	alternate_allele	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RASSF1	NM_170714	exon6	c.G941C	p.R314P	TCCTCCCGCTGCA	.	60.0	12.0	79.0	0.0	.	46	.	C|1.000;T|0.000	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	hg19	3	52429610	52429610	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DNAH1	NM_015512	exon70	c.A11175G	p.K3725K	GGGCAAATGGGTC	.	93.0	4.0	126.0	0.0	.	534	.	.	Atlas-SNP
CACNA1D	776	hgsc.bcm.edu	hg19	3	53839136	53839136	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CACNA1D	NM_000720	exon46	c.A5772G	p.R1924R	ACGGAGATCTCCA	.	29.0	4.0	41.0	0.0	.	324	.	.	Atlas-SNP
PRICKLE2	166336	hgsc.bcm.edu	hg19	3	64138962	64138962	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PRICKLE2	NM_198859	exon6	c.T683C	p.V228A	CCCAGCACTGTCT	.	98.0	4.0	73.0	0.0	.	88	.	.	Atlas-SNP
VGLL3	389136	hgsc.bcm.edu	hg19	3	87027732	87027732	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	VGLL3	NM_016206	exon2	c.T347C	p.L116P	GGATGGAGGGTGA	.	117.0	6.0	68.0	0.0	.	62	.	.	Atlas-SNP
IFT57	55081	hgsc.bcm.edu	hg19	3	107940994	107940994	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	IFT57	NM_018010	exon1	c.A176G	p.E59G	AGGAACTCCTCCT	.	95.0	5.0	114.0	0.0	.	44	.	.	Atlas-SNP
RETNLB	84666	hgsc.bcm.edu	hg19	3	108475432	108475432	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RETNLB	NM_032579	exon2	c.A131G	p.Y44C	GGACTGTACTCTG	.	81.0	4.0	113.0	0.0	.	38	.	.	Atlas-SNP
DPPA2	151871	hgsc.bcm.edu	hg19	3	109028179	109028179	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DPPA2	NM_138815	exon5	c.182-2A>G	.	ATGACCTAAGACA	.	124.0	5.0	210.0	0.0	.	52	.	.	Atlas-SNP
WDR5B	54554	hgsc.bcm.edu	hg19	3	122133628	122133628	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	WDR5B	NM_019069	exon1	c.G748A	p.G250S	TATGACCAGTGTA	.	114.0	5.0	169.0	0.0	.	36	.	.	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	hg19	3	126739124	126739124	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PLXNA1	NM_032242	exon20	c.G3975T	p.R1325R	CTACCGGACATAT	.	87.0	4.0	106.0	0.0	.	185	.	.	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	hg19	3	130285737	130285737	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	COL6A6	NM_001102608	exon4	c.A1474G	p.K492E	ATCAATAAATACT	.	123.0	5.0	148.0	0.0	.	497	.	.	Atlas-SNP
PIK3R4	30849	hgsc.bcm.edu	hg19	3	130435261	130435261	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	PIK3R4,NS,carcinoma,0,1	PIK3R4	NM_014602	exon9	c.T2310C	p.L770L	CTTCAGAAGCTGT	.	113.0	6.0	134.0	0.0	.	145	.	.	Atlas-SNP
RAB6B	51560	hgsc.bcm.edu	hg19	3	133560224	133560224	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RAB6B	NM_016577	exon4	c.A194G	p.Q65R	CAGAGCTGCAGTC	.	84.0	4.0	83.0	0.0	.	36	.	.	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	hg19	3	135721457	135721457	+	Missense_Mutation	SNP	T	T	C	rs148236440	alternate_allele	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PPP2R3A	NM_002718	exon2	c.T1117C	p.S373P	AACAACTCCACAA	.	119.0	5.0	135.0	0.0	.	114	.	T|1.000;G|0.000	Atlas-SNP
DBR1	51163	hgsc.bcm.edu	hg19	3	137880850	137880850	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DBR1	NM_016216	exon8	c.A1516T	p.T506S	CCTTGGTTAAGTC	.	540.0	194.0	602.0	0.0	.	45	.	.	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	hg19	3	145795696	145795696	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PLOD2	NM_182943	exon14	c.A1516G	p.K506E	AGTCTTTTTCCCT	.	57.0	4.0	41.0	0.0	.	81	.	.	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	hg19	3	150874118	150874118	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	MED12L,NS,carcinoma,0,1	MED12L	NM_053002	exon5	c.726+1G>A	.	TTCCAGGTAACCT	.	71.0	3.0	99.0	0.0	.	271	.	.	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	hg19	3	151154684	151154684	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	IGSF10	NM_178822	exon6	c.T7665C	p.V2555V	CTTGGGAACTCCC	.	144.0	6.0	170.0	0.0	.	279	.	.	Atlas-SNP
LEKR1	389170	hgsc.bcm.edu	hg19	3	156763334	156763334	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LEKR1	NM_001004316	exon13	c.T1874C	p.L625P	CAAGACTGAACTC	.	92.0	4.0	103.0	0.0	.	66	.	.	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	hg19	3	171965470	171965470	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	FNDC3B,NS,carcinoma,0,1	FNDC3B	NM_001135095	exon5	c.C412T	p.H138Y	AACTCACACACGG	.	263.0	101.0	289.0	0.0	.	118	.	.	Atlas-SNP
GHSR	2693	hgsc.bcm.edu	hg19	3	172163000	172163000	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GHSR	NM_198407	exon2	c.T1052C	p.L351P	TCTTTCAGAGTGG	.	78.0	4.0	84.0	0.0	.	104	.	.	Atlas-SNP
DCUN1D1	54165	hgsc.bcm.edu	hg19	3	182665120	182665120	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DCUN1D1	NM_020640	exon6	c.A606G	p.E202E	ATGATGTTCCTAT	.	90.0	4.0	107.0	0.0	.	27	.	.	Atlas-SNP
EIF4G1	1981	hgsc.bcm.edu	hg19	3	184049876	184049876	+	Splice_Site	SNP	T	T	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	EIF4G1	NM_001194946	exon33	c.4639+2T>A	.	TCCCAGTAAGAGC	.	65.0	4.0	88.0	0.0	.	151	.	.	Atlas-SNP
MAP3K13	9175	hgsc.bcm.edu	hg19	3	185191353	185191353	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.,1	MAP3K13	NM_004721	exon11	c.T2234C	p.I745T	TAGACATACCCTC	.	54.0	3.0	60.0	0.0	.	209	.	.	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	hg19	4	1805419	1805419	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FGFR3	NM_000142	exon8	c.A931G	p.T311A	TTGTAGACGGCGG	.	68.0	5.0	127.0	0.0	.	3320	.	.	Atlas-SNP
LETM1	3954	hgsc.bcm.edu	hg19	4	1843301	1843301	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	LETM1,caecum,carcinoma,0,1	LETM1	NM_012318	exon3	c.T367C	p.S123P	TGAGGGACTTCTC	.	52.0	4.0	73.0	0.0	.	48	.	.	Atlas-SNP
POLN	353497	hgsc.bcm.edu	hg19	4	2210196	2210196	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	POLN	NM_181808	exon3	c.A232G	p.S78G	TCTGACTTCTTAA	.	59.0	4.0	78.0	0.0	.	82	.	.	Atlas-SNP
SH3BP2	6452	hgsc.bcm.edu	hg19	4	2824742	2824742	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SH3BP2	NM_001145856	exon3	c.T388C	p.F130L	GGCGCCTTCTCCC	.	95.0	4.0	128.0	0.0	.	43	.	.	Atlas-SNP
LAP3	51056	hgsc.bcm.edu	hg19	4	17586728	17586728	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LAP3	NM_015907	exon6	c.A673G	p.S225G	CTCAAAAGTGCTA	.	99.0	4.0	110.0	0.0	.	50	.	.	Atlas-SNP
FAM184B	27146	hgsc.bcm.edu	hg19	4	17641002	17641002	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FAM184B	NM_015688	exon14	c.A2537G	p.Q846R	GCTTGCTGAGTCT	.	85.0	4.0	105.0	0.0	.	38	.	.	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	hg19	4	38830367	38830367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TLR6	NM_006068	exon2	c.C728T	p.S243L	AGTTCTGATAAAA	.	86.0	4.0	132.0	0.0	.	67	.	.	Atlas-SNP
PHOX2B	8929	hgsc.bcm.edu	hg19	4	41750513	41750513	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PHOX2B	NM_003924	exon1	c.G115A	p.A39T	CACTGGCCTGGCT	.	70.0	4.0	66.0	0.0	.	53	.	.	Atlas-SNP
ART3	419	hgsc.bcm.edu	hg19	4	77018798	77018798	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ART3	NM_001130017	exon4	c.A783G	p.G261G	TTCAGGACTAAAA	.	97.0	4.0	139.0	0.0	.	34	.	.	Atlas-SNP
AFF1	4299	hgsc.bcm.edu	hg19	4	88035706	88035706	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	AFF1	NM_001166693	exon12	c.C1721A	p.S574Y	AAAGCTCCAGCAA	.	62.0	17.0	76.0	0.0	.	102	.	.	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	hg19	4	94006348	94006348	+	Silent	SNP	T	T	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GRID2	NM_001510	exon3	c.T447G	p.P149P	CCCACCTGTCTAC	.	136.0	53.0	193.0	0.0	.	233	.	.	Atlas-SNP
PDHA2	5161	hgsc.bcm.edu	hg19	4	96761829	96761829	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PDHA2	NM_005390	exon1	c.T528C	p.A176A	CATTGCTCTGGCC	.	75.0	4.0	72.0	0.0	.	118	.	.	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	hg19	4	104053878	104053878	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CENPE	NM_001813	exon42	c.T6896A	p.V2299E	TTATTCACTTGAC	.	236.0	92.0	348.0	0.0	.	253	.	.	Atlas-SNP
ANK2	287	hgsc.bcm.edu	hg19	4	114274414	114274414	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ANK2	NM_001148	exon38	c.A4640G	p.E1547G	CAGGAGAGCCTTT	.	106.0	5.0	121.0	0.0	.	576	.	.	Atlas-SNP
PDE5A	8654	hgsc.bcm.edu	hg19	4	120549709	120549709	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PDE5A	NM_001083	exon1	c.T118C	p.F40L	AGGTAAAGTCCCA	.	75.0	5.0	76.0	0.0	.	83	.	.	Atlas-SNP
LARP1B	55132	hgsc.bcm.edu	hg19	4	129127685	129127685	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LARP1B	NM_018078	exon18	c.C2412A	p.Y804X	AGACTACGAATCT	.	76.0	4.0	103.0	0.0	.	120	.	.	Atlas-SNP
GAB1	2549	hgsc.bcm.edu	hg19	4	144378870	144378870	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GAB1	NM_207123	exon7	c.T1623C	p.G541G	CCATGGTTTAGAG	.	94.0	5.0	107.0	0.0	.	80	.	.	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	hg19	4	148563937	148563937	+	Splice_Site	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PRMT10	NM_138364	exon11	c.2199+1G>A	.	CACTTACCTGAAA	.	78.0	4.0	128.0	0.0	.	68	.	.	Atlas-SNP
NR3C2	4306	hgsc.bcm.edu	hg19	4	149073680	149073680	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NR3C2	NM_000901	exon6	c.G2450T	p.R817I	TACGATCTCCAGC	.	234.0	78.0	308.0	0.0	.	94	.	.	Atlas-SNP
RBM46	166863	hgsc.bcm.edu	hg19	4	155719149	155719149	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RBM46	NM_144979	exon3	c.A338G	p.E113G	AAGAAGAAGCCCA	.	100.0	4.0	159.0	0.0	.	76	.	.	Atlas-SNP
GALNTL6	442117	hgsc.bcm.edu	hg19	4	173730521	173730521	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GALNTL6	NM_001034845	exon6	c.A563G	p.K188R	ACCTGAAGGATAA	.	97.0	4.0	171.0	0.0	.	102	.	.	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	hg19	4	178257425	178257425	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	NEIL3	NM_018248	exon4	c.A577G	p.I193V	GGGAACATCATCA	.	94.0	4.0	174.0	0.0	.	89	.	.	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	hg19	4	184169911	184169911	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	WWC2	NM_024949	exon7	c.T777C	p.I259I	GAACATTGGCAGA	.	97.0	5.0	116.0	0.0	.	78	.	.	Atlas-SNP
UFSP2	55325	hgsc.bcm.edu	hg19	4	186336995	186336995	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	UFSP2	NM_018359	exon5	c.G360A	p.M120I	TTCCAGCATAAGA	.	79.0	4.0	126.0	0.0	.	33	.	.	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	hg19	4	187541014	187541014	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FAT1	NM_005245	exon10	c.G6726A	p.L2242L	AAAGTCCAGAGGA	.	76.0	4.0	168.0	0.0	.	500	.	.	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	hg19	5	488453	488453	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SLC9A3	NM_004174	exon3	c.T653C	p.L218P	TTCAGCAGCGACT	.	89.0	4.0	84.0	0.0	.	89	.	.	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	hg19	5	9119234	9119234	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SEMA5A	NM_003966	exon15	c.T1801C	p.W601R	AGGTCCAGGGAGT	.	140.0	7.0	122.0	0.0	.	236	.	.	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	hg19	5	14474101	14474101	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TRIO	NM_007118	exon40	c.5980-2A>G	.	AATTGTAGGGCTA	.	92.0	4.0	110.0	0.0	.	305	.	.	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	hg19	5	14502746	14502746	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TRIO	NM_007118	exon54	c.T8391C	p.S2797S	CTACAGTGAAGTG	.	69.0	5.0	60.0	0.0	.	305	.	.	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	hg19	5	14508302	14508302	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TRIO	NM_007118	exon57	c.A9065G	p.K3022R	GCCAGAAGGCCAA	.	64.0	4.0	90.0	0.0	.	305	.	.	Atlas-SNP
ZFR	51663	hgsc.bcm.edu	hg19	5	32444759	32444759	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ZFR	NM_016107	exon1	c.T6G	p.I2M	TATGGGAATCATG	.	326.0	36.0	223.0	0.0	.	98	.	.	Atlas-SNP
RICTOR	253260	hgsc.bcm.edu	hg19	5	38978735	38978735	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RICTOR	NM_152756	exon9	c.T771A	p.Y257X	ATCAGTATAGGGT	.	99.0	4.0	92.0	0.0	.	182	.	.	Atlas-SNP
SKIV2L2	23517	hgsc.bcm.edu	hg19	5	54674959	54674959	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SKIV2L2	NM_015360	exon18	c.A1988G	p.K663R	AGGTAAAGAATGA	.	36.0	4.0	32.0	0.0	.	104	.	.	Atlas-SNP
RGS7BP	401190	hgsc.bcm.edu	hg19	5	63802520	63802520	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	RGS7BP	NM_001029875	exon1	c.C69A	p.I23I	CCAGATCAGCAAG	.	115.0	5.0	84.0	0.0	.	32	.	.	Atlas-SNP
ADAMTS6	11174	hgsc.bcm.edu	hg19	5	64558682	64558682	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ADAMTS6	NM_197941	exon13	c.A1728G	p.G576G	GACGCCTCCCCCG	.	88.0	4.0	53.0	0.0	.	174	.	.	Atlas-SNP
CCNB1	891	hgsc.bcm.edu	hg19	5	68467214	68467214	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CCNB1	NM_031966	exon4	c.G481A	p.G161R	GAAGATGGAGCTG	.	286.0	88.0	237.0	0.0	.	36	.	.	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	hg19	5	82807955	82807955	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	VCAN	NM_004385	exon6	c.T782C	p.F261S	GTAAATTCACCTT	.	65.0	5.0	59.0	0.0	.	498	.	.	Atlas-SNP
MCTP1	79772	hgsc.bcm.edu	hg19	5	94224673	94224673	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MCTP1	NM_024717	exon12	c.C1844T	p.P615L	CTCAATGGGCTCT	.	108.0	5.0	91.0	0.0	.	110	.	.	Atlas-SNP
FTMT	94033	hgsc.bcm.edu	hg19	5	121187671	121187671	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FTMT	NM_177478	exon1	c.T13C	p.F5L	TCCTGCTTCAGGC	.	76.0	4.0	60.0	0.0	.	71	.	.	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	hg19	5	138260967	138260967	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	CTNNA1	NM_001903	exon13	c.A1770G	p.Q590Q	TGAGCAAGTAGAA	.	97.0	5.0	75.0	0.0	.	114	.	.	Atlas-SNP
DND1	373863	hgsc.bcm.edu	hg19	5	140052972	140052972	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	DND1	NM_194249	exon2	c.T26C	p.L9P	CACCACAGCTGAG	.	122.0	6.0	97.0	0.0	.	15	.	.	Atlas-SNP
PCDHB5	26167	hgsc.bcm.edu	hg19	5	140515856	140515856	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PCDHB5	NM_015669	exon1	c.T840C	p.A280A	CTATGCTCTATTC	.	99.0	4.0	100.0	0.0	.	184	.	.	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	hg19	5	140530199	140530199	+	Nonsense_Mutation	SNP	C	C	T	rs144886449	alternate_allele	TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PCDHB6	NM_018939	exon1	c.C361T	p.R121X	TCCTTGCGAGTCA	.	93.0	4.0	89.0	0.0	.	161	.	C|1.000;A|0.000	Atlas-SNP
PCDHGC3	5098	hgsc.bcm.edu	hg19	5	140856091	140856091	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	PCDHGC3	NM_032402	exon1	c.T408C	p.P136P	TTTCCCTACCCAG	.	119.0	5.0	120.0	0.0	.	173	.	.	Atlas-SNP
SH3TC2	79628	hgsc.bcm.edu	hg19	5	148407517	148407517	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SH3TC2	NM_024577	exon11	c.A1778G	p.E593G	GCCTTTTCCAACA	.	81.0	4.0	81.0	0.0	.	178	.	.	Atlas-SNP
ARHGEF37	389337	hgsc.bcm.edu	hg19	5	148980772	148980772	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ARHGEF37	NM_001001669	exon3	c.A288G	p.E96E	CAAGGAAGAGGAA	.	100.0	4.0	86.0	0.0	.	45	.	.	Atlas-SNP
TNIP1	10318	hgsc.bcm.edu	hg19	5	150436496	150436496	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TNIP1	NM_001252385	exon6	c.A458G	p.E153G	CCGTCCTCACGGG	.	61.0	5.0	38.0	0.0	.	51	.	.	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	hg19	5	160063301	160063301	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	ATP10B	NM_025153	exon11	c.A1016G	p.N339S	GTCCCATTCCAGA	.	85.0	4.0	65.0	0.0	.	201	.	.	Atlas-SNP
GABRG2	2566	hgsc.bcm.edu	hg19	5	161580269	161580269	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GABRG2	NM_198903	exon11	c.G1443A	p.R481R	TGGGAGGATACAT	.	716.0	200.0	589.0	0.0	.	142	.	.	Atlas-SNP
FAM193B	54540	hgsc.bcm.edu	hg19	5	176951436	176951436	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	FAM193B	NM_001190946	exon6	c.A2046G	p.K682K	GCCTACTTTGGGA	.	99.0	5.0	129.0	0.0	.	28	.	.	Atlas-SNP
TBC1D9B	23061	hgsc.bcm.edu	hg19	5	179320450	179320450	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TBC1D9B	NM_198868	exon5	c.T595C	p.W199R	CCACCCACTGCAC	.	72.0	4.0	64.0	0.0	.	157	.	.	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	hg19	5	180218962	180218962	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	MGAT1	NM_001114617	exon3	c.A1010G	p.Q337R	ACAAACTGCTGGT	.	89.0	4.0	88.0	0.0	.	48	.	.	Atlas-SNP
SLC22A23	63027	hgsc.bcm.edu	hg19	6	3290023	3290023	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	SLC22A23	NM_015482	exon6	c.A1288G	p.N430D	CAATGTTCTTCCA	.	84.0	4.0	88.0	0.0	.	89	.	.	Atlas-SNP
TMPRSS11B	132724	hgsc.bcm.edu	hg19	4	69097023	69097023	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	TMPRSS11B	NM_182502	exon7	c.585delA	p.A195fs	.	.	241.0	76.0	187.0	0.0	.	66	.	.	Atlas-Indel,Pindel
WDR33	55339	hgsc.bcm.edu	hg19	2	128522284	128522336	+	Frame_Shift_Del	DEL	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	-	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	GTGCAGAAAGTTTCCCAGAAACTGACAGAGCCCATGCATCTCTGCACCCAGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	WDR33	NM_001006622	exon6	c.693_745del	p.231_249del	.	.	155.0	16.0	271.0	0.0	.	136	.	.	Atlas-Indel,Pindel
GABRG2	2566	hgsc.bcm.edu	hg19	5	161576259	161576259	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	GABRG2	NM_198903	exon9	c.1187delT	p.L396fs	.	.	915.0	222.0	807.0	0.0	.	142	.	.	Atlas-Indel,Pindel
LEAP2	116842	hgsc.bcm.edu	hg19	5	132209684	132209685	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	LEAP2	NM_052971	exon2	c.100_101insG	p.R34fs	.	.	136.0	64.0	137.0	0.0	.	6	.	.	Atlas-Indel,Pindel
UBQLN4	56893	hgsc.bcm.edu	hg19	1	156011369	156011371	+	In_Frame_Del	DEL	CGT	CGT	-	novel		TCGA-BC-A10W-01A-11D-A12Z-10	TCGA-BC-A10W-11A-11D-A12Z-10	CGT	CGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9681d501-d5be-4b4d-8587-69b0a4f9eb3a	16c0da05-13b9-4c80-947f-2532f2cbf61a	.	UBQLN4	NM_020131	exon10	c.1559_1561del	p.520_521del	.	.	403.0	45.0	152.0	0.0	.	47	.	.	Atlas-INDEL
