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	Algorithm
PCM1	5108	hgsc.bcm.edu	37	8	17796494	17796496	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCM1	NM_006197	exon5	c.587_589del	p.196_197del	.	.	197.0	96.0	149.0	0.0	.	.	Atlas-Indel,Pindel
HOMEZ	57594	hgsc.bcm.edu	37	14	23745661	23745666	+	In_Frame_Del	DEL	GCTTGT	GCTTGT	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	GCTTGT	GCTTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HOMEZ	NM_020834	exon2	c.772_777del	p.258_259del	.	.	218.0	40.0	62.0	0.0	.	.	Atlas-Indel
RBM33	155435	hgsc.bcm.edu	37	7	155532429	155532430	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RBM33	NM_053043	exon12	c.1758_1759insC	p.L586fs	.	.	73.0	11.0	37.0	0.0	.	.	Atlas-Indel
CFH	3075	hgsc.bcm.edu	37	1	196642196	196642200	+	Frame_Shift_Del	DEL	CTATA	CTATA	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	CTATA	CTATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CFH	NM_001014975	exon2	c.146_150del	p.49_50del	.	.	241.0	68.0	110.0	0.0	.	.	Atlas-Indel,Pindel
MTOR	2475	hgsc.bcm.edu	37	1	11190693	11190694	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MTOR	NM_004958	exon39	c.5506_5507insC	p.A1836fs	.	.	182.0	15.0	99.0	0.0	.	.	Atlas-Indel
SYNE3	161176	hgsc.bcm.edu	37	14	95916347	95916348	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_152592	exon7	c.1370_1371insG	p.A457fs	.	.	146.0	12.0	66.0	0.0	.	.	Atlas-Indel
SF3B4	10262	hgsc.bcm.edu	37	1	149895825	149895826	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SF3B4	NM_005850	exon5	c.995_996insC	p.Q332fs	.	.	115.0	12.0	25.0	0.0	.	.	Atlas-Indel
ZFPM1	161882	hgsc.bcm.edu	37	16	88598517	88598518	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZFPM1	NM_153813	exon7	c.820_821insC	p.A274fs	.	.	175.0	11.0	104.0	0.0	.	.	Atlas-Indel
FAM211B	388886	hgsc.bcm.edu	37	22	24982055	24982057	+	In_Frame_Del	DEL	GTT	GTT	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_207644	exon4	c.746_748del	p.249_250del	.	.	53.0	16.0	40.0	0.0	.	.	Atlas-Indel
USP9X	8239	hgsc.bcm.edu	37	X	41027391	41027394	+	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	AGTA	AGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USP9X	NM_001039591	exon18	c.2555_2558del	p.852_853del	.	.	257.0	153.0	101.0	0.0	.	.	Atlas-Indel,Pindel
GLIS1	148979	hgsc.bcm.edu	37	1	53975643	53975644	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GLIS1	NM_147193	exon8	c.1416_1417insC	p.P472fs	.	.	195.0	23.0	69.0	0.0	.	.	Atlas-Indel
CKAP2L	150468	hgsc.bcm.edu	37	2	113509890	113509890	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CKAP2L	NM_152515	exon5	c.1557delT	p.S519fs	.	.	1092.0	356.0	378.0	0.0	.	.	Atlas-Indel
POLR3C	10623	hgsc.bcm.edu	37	1	145601821	145601822	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	POLR3C	NM_006468	exon6	c.710_711insG	p.A237fs	.	.	221.0	16.0	81.0	0.0	.	.	Atlas-Indel
MYH2	4620	hgsc.bcm.edu	37	17	10432501	10432501	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MYH2	NM_017534	exon26	c.3333delG	p.Q1111fs	.	.	246.0	90.0	63.0	0.0	.	.	Atlas-Indel,Pindel
NDUFB11	54539	hgsc.bcm.edu	37	X	47003944	47003945	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NDUFB11	NM_019056	exon1	c.135_136insG	p.G45fs	.	.	139.0	13.0	30.0	0.0	.	.	Atlas-Indel
ATAD3A	55210	hgsc.bcm.edu	37	1	1458209	1458210	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATAD3A	NM_018188	exon8	c.980_981insG	p.L327fs	.	.	203.0	13.0	107.0	0.0	.	.	Atlas-Indel
KIAA1432	57589	hgsc.bcm.edu	37	9	5753230	5753231	+	Frame_Shift_Del	DEL	CC	CC	-	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIAA1432	NM_001135920	exon13	c.1482_1483del	p.494_495del	.	.	747.0	165.0	328.0	0.0	.	.	Atlas-Indel
PPP1R15B	84919	hgsc.bcm.edu	37	1	204379574	204379575	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPP1R15B	NM_032833	exon1	c.966_967insA	p.Y322_H323delinsX	.	.	367.0	23.0	116.0	0.0	.	.	Atlas-Indel
RIMS1	22999	hgsc.bcm.edu	37	6	73100382	73100383	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RIMS1	NM_014989	exon30	c.4449_4450insC	p.R1483fs	.	.	148.0	13.0	71.0	0.0	.	.	Atlas-Indel
RFPL2	10739	hgsc.bcm.edu	37	22	32588962	32588963	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RFPL2	NM_001098527	exon4	c.483_484insG	p.A161fs	.	.	274.0	19.0	115.0	0.0	.	.	Atlas-Indel
BAG6	7917	hgsc.bcm.edu	37	6	31609641	31609642	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BAG6	NM_004639	exon16	c.2327_2328insC	p.Q776fs	.	.	105.0	13.0	44.0	0.0	.	.	Atlas-Indel
WISP3	8838	hgsc.bcm.edu	37	6	112382364	112382364	+	Silent	SNP	A	A	T	rs139375158		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WISP3	NM_198239	exon2	c.A273T	p.G91G	CTGTGGATGCTGT	.	222.0	13.0	94.0	0.0	A|1.000;T|0.000	.	Atlas-SNP
FNIP1	96459	hgsc.bcm.edu	37	5	131054750	131054750	+	Silent	SNP	G	G	A	rs61738669	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FNIP1	NM_001008738	exon5	c.C459T	p.S153S	TGGAGGGGAACTA	.	199.0	8.0	99.0	0.0	G|0.984;A|0.016	.	Atlas-SNP
PRKCD	5580	hgsc.bcm.edu	37	3	53218895	53218895	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRKCD	NM_212539	exon9	c.G793A	p.G265S	GACTGCGGCATGA	.	174.0	7.0	32.0	0.0	.	.	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108074043	108074043	+	Missense_Mutation	SNP	G	G	A	rs147302228		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HHLA2	NM_007072	exon5	c.G500A	p.R167H	ATCCTCGTCCAAT	.	244.0	10.0	96.0	0.0	G|0.994;A|0.006	.	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135743593	135743593	+	Missense_Mutation	SNP	T	T	C	rs79528341	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_025052	exon7	c.A2849G	p.N950S	ATTGAATTTGTGC	.	705.0	33.0	307.0	0.0	T|0.994;C|0.006	.	Atlas-SNP
BEND2	139105	hgsc.bcm.edu	37	X	18221980	18221980	+	Missense_Mutation	SNP	C	C	A	rs75342823	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BEND2	NM_001184767	exon5	c.G548T	p.S183I	GCAGGGCTGGCCC	.	172.0	10.0	41.0	0.0	C|0.970;A|0.030	.	Atlas-SNP
C19orf47	126526	hgsc.bcm.edu	37	19	40834394	40834394	+	Missense_Mutation	SNP	C	C	T	rs9973304	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C19orf47	NM_001256440	exon6	c.G476A	p.R159H	TCCGGGCGCCTGG	.	227.0	16.0	67.0	0.0	C|0.992;T|0.008	.	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66430086	66430086	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CDH5	NM_001795	exon8	c.A1342G	p.K448E	GAGGCCAAAGAAC	.	92.0	32.0	41.0	0.0	.	.	Atlas-SNP
MUSK	4593	hgsc.bcm.edu	37	9	113538072	113538072	+	Missense_Mutation	SNP	T	T	C	rs79843573	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MUSK	NM_005592	exon9	c.T1189C	p.Y397H	AGAGAGTACTGCT	.	242.0	11.0	97.0	0.0	T|0.993;C|0.007	.	Atlas-SNP
EFCAB7	84455	hgsc.bcm.edu	37	1	63991322	63991322	+	Missense_Mutation	SNP	T	T	A	rs17125106	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EFCAB7	NM_032437	exon2	c.T79A	p.F27I	AAGAAATTTCCAC	.	296.0	28.0	132.0	0.0	T|0.974;A|0.026	.	Atlas-SNP
SGCG	6445	hgsc.bcm.edu	37	13	23898556	23898556	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SGCG	NM_000231	exon8	c.C752A	p.T251K	AGGGGACGTGGGG	.	111.0	38.0	28.0	0.0	.	.	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58757695	58757695	+	Silent	SNP	G	G	A	rs8059441	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GOT2	NM_002080	exon2	c.C201T	p.Y67Y	ATCCCGGTAGGCA	.	273.0	14.0	124.0	0.0	G|0.979;A|0.021	.	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120381975	120381975	+	Missense_Mutation	SNP	G	G	T	rs202036468		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NBPF7	NM_001047980	exon5	c.C670A	p.L224M	CCTCCAGTGAGTC	.	527.0	27.0	208.0	0.0	G|0.999;T|0.001	.	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117044586	117044586	+	Silent	SNP	C	C	T	rs200162485		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COL27A1	NM_032888	exon38	c.C3747T	p.G1249G	GCAAGGCGAGAAG	.	191.0	13.0	50.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
MCM3AP	8888	hgsc.bcm.edu	37	21	47695223	47695223	+	Silent	SNP	G	G	A	rs145653489	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MCM3AP	NM_003906	exon6	c.C1875T	p.T625T	CAGATCGGTTCTC	.	91.0	6.0	38.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71386481	71386481	+	Silent	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SDK2	NM_001144952	exon29	c.C4137G	p.T1379T	CTTGCGGGTCTGG	.	108.0	39.0	54.0	0.0	.	.	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40902272	40902272	+	Missense_Mutation	SNP	G	G	A	rs149183991	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRX	NM_181882	exon7	c.C1987T	p.P663S	TCTCTGGGACTTT	.	135.0	7.0	35.0	0.0	G|1.000;A|0.000	.	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95381757	95381757	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PDE6C	NM_006204	exon4	c.G792A	p.A264A	CAAAGCGCTCTAC	.	136.0	16.0	44.0	0.0	.	.	Atlas-SNP
C3orf37	56941	hgsc.bcm.edu	37	3	129020853	129020853	+	Silent	SNP	C	C	T	rs114999931	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C3orf37	NM_020187	exon6	c.C696T	p.V232V	TGAAGTCTCAACT	.	156.0	11.0	59.0	0.0	C|0.990;T|0.010	.	Atlas-SNP
CSRP1	1465	hgsc.bcm.edu	37	1	201459399	201459399	+	Silent	SNP	G	G	A	rs504667	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CSRP1	NM_001193572	exon3	c.C186T	p.Y62Y	CTTGCCGTAGCAG	.	170.0	10.0	46.0	0.0	G|0.974;A|0.026	.	Atlas-SNP
SEC23B	10483	hgsc.bcm.edu	37	20	18506558	18506558	+	Silent	SNP	T	T	C	rs115177758	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SEC23B	NM_032985	exon7	c.T816C	p.I272I	GTCCATTGCTGTT	.	293.0	19.0	87.0	0.0	T|0.992;C|0.008	.	Atlas-SNP
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839941	27839941	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HIST1H3I	NM_003533	exon1	c.G153C	p.E51D	GCGGATCTCGCGC	.	120.0	37.0	60.0	0.0	.	.	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62269392	62269392	+	Missense_Mutation	SNP	G	G	T	rs115290371	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	VPS13C	NM_020821	exon24	c.C2297A	p.T766N	TTCCAGGTTTCCT	.	270.0	13.0	88.0	0.0	G|0.987;T|0.013	.	Atlas-SNP
SUCO	51430	hgsc.bcm.edu	37	1	172520658	172520658	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_014283	exon2	c.C69T	p.P23P	GCTTCCCAGCTGG	.	162.0	53.0	38.0	0.0	.	.	Atlas-SNP
TNFRSF17	608	hgsc.bcm.edu	37	16	12060114	12060114	+	Missense_Mutation	SNP	A	A	G	rs11570147	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TNFRSF17	NM_001192	exon2	c.A193G	p.I65V	AGCTTAATAATTT	.	370.0	15.0	125.0	0.0	A|0.998;G|0.002	.	Atlas-SNP
FAM127C	441518	hgsc.bcm.edu	37	X	134156292	134156292	+	Silent	SNP	C	C	G	rs190970621		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FAM127C	NM_001078173	exon1	c.G198C	p.T66T	GAGGAACGTCACC	.	160.0	12.0	64.0	0.0	C|0.981;G|0.019	.	Atlas-SNP
EEFSEC	60678	hgsc.bcm.edu	37	3	128127053	128127053	+	Missense_Mutation	SNP	T	T	G	rs114096655	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EEFSEC	NM_021937	exon7	c.T1742G	p.F581C	TGACTTTCAAGCG	.	258.0	13.0	85.0	0.0	T|0.992;G|0.008	.	Atlas-SNP
MAOB	4129	hgsc.bcm.edu	37	X	43656384	43656384	+	Silent	SNP	T	T	C	rs7879356	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MAOB	NM_000898	exon6	c.A606G	p.T202T	TCCATTTGTTGTC	.	224.0	15.0	70.0	0.0	0|0.072;C|0.055	.	Atlas-SNP
ACTN2	88	hgsc.bcm.edu	37	1	236918483	236918483	+	Silent	SNP	G	G	A	rs34975493	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ACTN2	NM_001103	exon17	c.G2139A	p.T713T	GCACACGAACTAC	.	108.0	7.0	57.0	0.0	G|0.969;A|0.031	.	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	929613	929613	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LMF1	NM_022773	exon6	c.G854A	p.R285Q	GCCCGCCGGCCGA	.	104.0	6.0	45.0	0.0	.	.	Atlas-SNP
CD22	933	hgsc.bcm.edu	37	19	35829220	35829220	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CD22	NM_001185100	exon6	c.G1135T	p.E379X	ACAGAGGAGAAAG	.	158.0	29.0	42.0	0.0	.	.	Atlas-SNP
C11orf30	56946	hgsc.bcm.edu	37	11	76255823	76255823	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C11orf30	NM_020193	exon19	c.A3230T	p.Q1077L	AGAGCCAAATGTC	.	58.0	27.0	19.0	0.0	.	.	Atlas-SNP
ACOX2	8309	hgsc.bcm.edu	37	3	58516293	58516293	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ACOX2	NM_003500	exon8	c.G892A	p.V298M	GCTCCACCCGCAC	.	213.0	69.0	75.0	0.0	.	.	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14952189	14952189	+	Silent	SNP	G	G	T	rs114596415	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR7A10	NM_001005190	exon1	c.C501A	p.P167P	ACAAAAGGGCAGT	.	138.0	12.0	75.0	0.0	G|0.980;T|0.020	.	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825206	95825206	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MAML2	NM_032427	exon2	c.G1989A	p.Q663Q	TTGTTGCTGCTGC	.	255.0	18.0	103.0	0.0	.	.	Atlas-SNP
TCP10	6953	hgsc.bcm.edu	37	6	167786673	167786673	+	Missense_Mutation	SNP	T	T	C	rs181671268		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TCP10	NM_004610	exon8	c.A965G	p.Q322R	ATGTCCTGTCTGG	.	171.0	9.0	77.0	0.0	T|0.999;C|0.001	.	Atlas-SNP
NOS2	4843	hgsc.bcm.edu	37	17	26107858	26107858	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NOS2	NM_000625	exon9	c.C939T	p.G313G	GTCACGGCCATTG	.	88.0	31.0	44.0	0.0	.	.	Atlas-SNP
DDX25	29118	hgsc.bcm.edu	37	11	125778305	125778305	+	Silent	SNP	C	C	T	rs34007659	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DDX25	NM_013264	exon6	c.C414T	p.N138N	CCAGAACCTCATA	.	235.0	11.0	97.0	0.0	C|0.985;T|0.015	.	Atlas-SNP
OR5K4	403278	hgsc.bcm.edu	37	3	98072715	98072715	+	Missense_Mutation	SNP	C	C	A	rs77559509	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5K4	NM_001005517	exon1	c.C18A	p.H6Q	AAATCACTCCTTA	.	279.0	12.0	108.0	0.0	C|0.976;A|0.024	.	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837008	43837008	+	Missense_Mutation	SNP	G	G	A	rs61730001	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SEMG1	NM_003007	exon2	c.G1070A	p.R357Q	AAAGACGACTCCA	.	330.0	17.0	180.0	0.0	G|0.985;A|0.015	.	Atlas-SNP
HYAL1	3373	hgsc.bcm.edu	37	3	50337945	50337945	+	Missense_Mutation	SNP	G	G	C	rs142342237	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HYAL1	NM_033159	exon4	c.C1277G	p.A426G	CACGGTGCCTGCC	.	187.0	10.0	52.0	0.0	G|0.994;C|0.006	.	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	709421	709421	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EPS8L2	NM_022772	exon2	c.G14T	p.G5V	AGTCCGGGGCCGT	.	93.0	26.0	34.0	0.0	.	.	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	87089307	87089307	+	Silent	SNP	G	G	A	rs61744083	byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_152336	exon19	c.G2622A	p.L874L	AACCTTGTGGCAA	.	371.0	25.0	129.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983401	97983401	+	Silent	SNP	C	C	T	rs113782472	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5H6	NM_001005479	exon1	c.C273T	p.S91S	ATCATCCACAGTG	.	928.0	52.0	313.0	0.0	C|0.978;T|0.022	.	Atlas-SNP
USP3	9960	hgsc.bcm.edu	37	15	63866314	63866314	+	Missense_Mutation	SNP	A	A	G	rs138310278	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USP3	NM_006537	exon10	c.A978G	p.I326M	CCTCATATGTGGG	.	300.0	15.0	97.0	0.0	A|1.000;G|0.000	.	Atlas-SNP
UBXN10	127733	hgsc.bcm.edu	37	1	20517834	20517834	+	Silent	SNP	G	G	A	rs77365331	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UBXN10	NM_152376	exon2	c.G780A	p.E260E	GCAAGAGTGCAGA	.	124.0	9.0	50.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26809429	26809429	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ITPR2	NM_002223	exon19	c.A2245G	p.I749V	GGTTTATGGCCAG	.	77.0	26.0	40.0	0.0	.	.	Atlas-SNP
B3GAT2	135152	hgsc.bcm.edu	37	6	71666019	71666019	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	B3GAT2	NM_080742	exon1	c.C114T	p.P38P	GAAGTAGGGGCGC	.	93.0	43.0	36.0	0.0	.	.	Atlas-SNP
ATXN7L1	222255	hgsc.bcm.edu	37	7	105264636	105264636	+	Silent	SNP	C	C	T	rs147354371	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATXN7L1	NM_020725	exon8	c.G1281A	p.P427P	TCCAACCGGTGGG	.	171.0	12.0	86.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
CRYGA	1418	hgsc.bcm.edu	37	2	209025671	209025671	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CRYGA	NM_014617	exon3	c.G382A	p.E128K	AGCCCTCCAGTAC	.	114.0	44.0	35.0	0.0	.	.	Atlas-SNP
PGLYRP4	57115	hgsc.bcm.edu	37	1	153309676	153309676	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PGLYRP4	NM_020393	exon8	c.C924A	p.T308T	CATGAAGGTAATG	.	65.0	26.0	23.0	0.0	.	.	Atlas-SNP
GBP6	163351	hgsc.bcm.edu	37	1	89835220	89835220	+	Silent	SNP	C	C	A	rs114110284	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GBP6	NM_198460	exon3	c.C306A	p.G102G	TCTGGGCGATGTG	.	137.0	9.0	66.0	0.0	C|0.980;A|0.020	.	Atlas-SNP
IQCD	115811	hgsc.bcm.edu	37	12	113645566	113645566	+	Missense_Mutation	SNP	G	G	C	rs7966313	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IQCD	NM_138451	exon2	c.C406G	p.L136V	TCTGCAGCTCTAT	.	161.0	10.0	64.0	0.0	G|0.994;C|0.006	.	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23909671	23909671	+	Missense_Mutation	SNP	C	C	T	rs61742502	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SACS	NM_014363	exon10	c.G8344A	p.A2782T	CAGATGCATGAAA	.	177.0	11.0	47.0	0.0	C|0.994;T|0.006	.	Atlas-SNP
C20orf194	25943	hgsc.bcm.edu	37	20	3233305	3233305	+	Silent	SNP	G	G	A	rs61744985	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C20orf194	NM_001009984	exon37	c.C3447T	p.Y1149Y	TTCCACGTAGTCA	.	312.0	14.0	126.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39913894	39913894	+	Missense_Mutation	SNP	G	G	A	rs61730570	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLEKHG2	NM_022835	exon18	c.G2200A	p.E734K	CCAGAGGAGGATG	.	195.0	9.0	60.0	0.0	G|0.994;A|0.006	.	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801713	14801713	+	Missense_Mutation	SNP	G	G	A	rs76714828		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FREM1	NM_144966	exon21	c.C3631T	p.P1211S	TGGCTGGCTGCTT	.	332.0	21.0	177.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
PWWP2A	114825	hgsc.bcm.edu	37	5	159519956	159519956	+	Silent	SNP	A	A	G	rs58423476	bycluster;byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PWWP2A	NM_001130864	exon2	c.T1701C	p.Y567Y	GGTCATATAAACA	.	612.0	27.0	254.0	0.0	A|0.989;G|0.011	.	Atlas-SNP
PLCD4	84812	hgsc.bcm.edu	37	2	219480468	219480468	+	Silent	SNP	G	G	A	rs7582929		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLCD4	NM_032726	exon2	c.G6A	p.A2A	GATGGCGTCCCTG	.	198.0	11.0	48.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
ATRX	546	hgsc.bcm.edu	37	X	76937966	76937966	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATRX	NM_000489	exon9	c.G2782C	p.E928Q	TCTGCTCTTTCCC	.	195.0	14.0	86.0	0.0	.	.	Atlas-SNP
RPL4	6124	hgsc.bcm.edu	37	15	66793310	66793310	+	Silent	SNP	G	G	A	rs73471768	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RPL4	NM_000968	exon7	c.C810T	p.A270A	GGAAGCGGCTTTA	.	388.0	16.0	158.0	0.0	G|0.992;A|0.008	.	Atlas-SNP
CPNE4	131034	hgsc.bcm.edu	37	3	131442432	131442432	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CPNE4	NM_130808	exon3	c.C218T	p.P73L	TACACTGGGTTTA	.	175.0	63.0	47.0	0.0	.	.	Atlas-SNP
PPP2R5E	5529	hgsc.bcm.edu	37	14	63881929	63881929	+	Silent	SNP	G	G	T	rs10133826	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPP2R5E	NM_006246	exon5	c.C478A	p.R160R	AAAATCGTATGAA	.	300.0	12.0	100.0	0.0	G|0.987;T|0.013	.	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183754538	183754538	+	Missense_Mutation	SNP	C	C	T	rs73050313	bycluster;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HTR3D	NM_001163646	exon5	c.C514T	p.R172W	CGAGCCCGGGCAT	.	115.0	7.0	42.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241436	3241436	+	Missense_Mutation	SNP	C	C	G	rs5983120	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MXRA5	NM_015419	exon5	c.G2290C	p.V764L	CAAACACTCTGCG	.	373.0	23.0	71.0	0.0	C|0.958;G|0.042	.	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64492098	64492098	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SYNE2	NM_182914	exon41	c.G6211C	p.E2071Q	TCATCCGAAGGCA	.	90.0	38.0	57.0	0.0	.	.	Atlas-SNP
OR2M3	127062	hgsc.bcm.edu	37	1	248367150	248367150	+	Missense_Mutation	SNP	C	C	T	rs147728074	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR2M3	NM_001004689	exon1	c.C781T	p.R261W	TACATACGGCCCA	.	376.0	20.0	138.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47365122	47365122	+	Missense_Mutation	SNP	G	G	A	rs11570076	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MYBPC3	NM_000256	exon13	c.C1144T	p.R382W	TCAGCCGGATCTT	.	119.0	9.0	29.0	0.0	G|0.987;A|0.013	.	Atlas-SNP
TLR2	7097	hgsc.bcm.edu	37	4	154625685	154625685	+	Silent	SNP	C	C	G	rs5743701	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TLR2	NM_003264	exon3	c.C1626G	p.L542L	ATTCCTCTCCTTC	.	321.0	13.0	62.0	0.0	C|0.989;G|0.011	.	Atlas-SNP
RLIM	51132	hgsc.bcm.edu	37	X	73814140	73814140	+	Splice_Site	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RLIM	NM_016120	exon4	c.253+1G>T	.	AACATACCTCTAT	.	126.0	80.0	46.0	0.0	.	.	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6867035	6867035	+	Missense_Mutation	SNP	A	A	T	rs7949377	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR10A5	NM_178168	exon1	c.A122T	p.K41M	CTCTGAAGGGAAA	.	357.0	22.0	156.0	0.0	A|0.986;T|0.014	.	Atlas-SNP
PATE3	100169851	hgsc.bcm.edu	37	11	125659320	125659320	+	Missense_Mutation	SNP	C	C	A	rs1025165		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001129883	exon2	c.C89A	p.T30K	TTCGCACACGGAC	.	109.0	8.0	32.0	0.0	C|0.998;A|0.002	.	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378932	31378932	+	Missense_Mutation	SNP	G	G	A	rs41556715	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001177519	exon3	c.G409A	p.G137R	TACGATGGGGAGC	.	172.0	7.0	62.0	0.0	G|0.989;A|0.011	.	Atlas-SNP
SPTBN2	6712	hgsc.bcm.edu	37	11	66481628	66481628	+	Missense_Mutation	SNP	T	T	C	rs148154681	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SPTBN2	NM_006946	exon6	c.A590G	p.N197S	TGTACATTGACGT	.	154.0	7.0	63.0	0.0	T|1.000;C|0.000	.	Atlas-SNP
PROC	5624	hgsc.bcm.edu	37	2	128186189	128186189	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PROC	NM_000312	exon9	c.G1053A	p.E351E	GAAGGAGGCCAAG	.	74.0	15.0	49.0	0.0	.	.	Atlas-SNP
TUBGCP6	85378	hgsc.bcm.edu	37	22	50656942	50656942	+	Silent	SNP	G	G	A	rs147939592	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TUBGCP6	NM_020461	exon22	c.C4929T	p.D1643D	GCAGACGTCCTTG	.	127.0	6.0	25.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	37	5	137754798	137754798	+	Missense_Mutation	SNP	G	G	T	rs28561931	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KDM3B	NM_016604	exon14	c.G3592T	p.A1198S	AGTTCGGCATCAA	.	251.0	14.0	109.0	0.0	G|0.990;T|0.010	.	Atlas-SNP
LRRC29	26231	hgsc.bcm.edu	37	16	67241545	67241545	+	Missense_Mutation	SNP	C	C	T	rs75503949	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LRRC29	NM_001004055	exon6	c.G635A	p.R212H	ACGAAGCGGGACT	.	81.0	8.0	29.0	0.0	C|0.995;T|0.005	.	Atlas-SNP
TAAR6	319100	hgsc.bcm.edu	37	6	132892143	132892143	+	Missense_Mutation	SNP	C	C	T	rs17061409	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TAAR6	NM_175067	exon1	c.C683T	p.A228V	GACAGGCGAAAAA	.	100.0	9.0	61.0	0.0	C|0.946;T|0.054	.	Atlas-SNP
LYZL2	119180	hgsc.bcm.edu	37	10	30915727	30915727	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LYZL2	NM_183058	exon2	c.T256A	p.W86R	AGCCCCAGTAATT	.	619.0	103.0	214.0	0.0	.	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228511298	228511298	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OBSCN	NM_001271223	exon67	c.C18514T	p.R6172C	GAGCTCCGTGTGG	.	165.0	8.0	65.0	0.0	.	.	Atlas-SNP
EPB41L4A	64097	hgsc.bcm.edu	37	5	111594953	111594953	+	Silent	SNP	T	T	C	rs34755755		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EPB41L4A	NM_022140	exon9	c.A768G	p.Q256Q	TTCAAATTGAGTC	.	209.0	10.0	77.0	0.0	T|0.020;G|0.005	.	Atlas-SNP
SUCLG2	8801	hgsc.bcm.edu	37	3	67578624	67578624	+	Missense_Mutation	SNP	C	C	T	rs13318110	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SUCLG2	NM_001177599	exon4	c.G349A	p.A117T	GTTTAGCCAGCTG	.	307.0	15.0	115.0	0.0	C|0.985;T|0.015	.	Atlas-SNP
ZBTB14	7541	hgsc.bcm.edu	37	18	5291304	5291304	+	Silent	SNP	C	C	T	rs34402690	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001243702	exon4	c.G903A	p.A301A	CCTGTCCGCCGTG	.	208.0	9.0	53.0	0.0	C|0.981;T|0.019	.	Atlas-SNP
KLHL40	131377	hgsc.bcm.edu	37	3	42729685	42729685	+	Missense_Mutation	SNP	C	C	T	rs149076152		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_152393	exon2	c.C1204T	p.R402C	TCGCCCCGCTGCC	.	211.0	9.0	56.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140594145	140594145	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDHB13	NM_018933	exon1	c.G450T	p.G150G	TCCTGGGACTACG	.	599.0	203.0	318.0	0.0	.	.	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25257468	25257468	+	Silent	SNP	C	C	T	rs141714689	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DOCK5	NM_024940	exon46	c.C4746T	p.D1582D	TGAAGACCAGGAG	.	108.0	9.0	54.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	37	4	39306471	39306471	+	Missense_Mutation	SNP	C	C	G	rs11932767	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RFC1	NM_001204747	exon15	c.G2076C	p.E692D	CAGTGACTCAGCA	.	204.0	10.0	56.0	0.0	C|0.979;G|0.021	.	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88782463	88782463	+	Silent	SNP	G	G	A	rs189107499	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001142864	exon50	c.C7194T	p.T2398T	GAAGCCGGTGGCC	.	89.0	7.0	27.0	0.0	G|0.994;A|0.006	.	Atlas-SNP
UTP18	51096	hgsc.bcm.edu	37	17	49365500	49365500	+	Missense_Mutation	SNP	C	C	T	rs61732669		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UTP18	NM_016001	exon11	c.C1439T	p.T480I	CTCTGACCTTCAA	.	442.0	32.0	196.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
FGF20	26281	hgsc.bcm.edu	37	8	16850601	16850601	+	Missense_Mutation	SNP	C	C	T	rs17550360	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FGF20	NM_019851	exon3	c.G616A	p.D206N	GTAGGTCCTTGTA	.	111.0	11.0	65.0	0.0	C|0.968;T|0.032	.	Atlas-SNP
EIF4E1B	253314	hgsc.bcm.edu	37	5	176072880	176072880	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001099408	exon9	c.G628T	p.E210X	TACAAAGAGCGCC	.	184.0	64.0	72.0	0.0	.	.	Atlas-SNP
C9orf37	85026	hgsc.bcm.edu	37	9	140510427	140510427	+	Silent	SNP	C	C	T	rs146719588	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C9orf37	NM_032937	exon3	c.G225A	p.P75P	AAACAACGGAGAT	.	147.0	8.0	54.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28887185	28887185	+	Silent	SNP	G	G	A	rs9900264	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TBC1D29	NM_015594	exon2	c.G63A	p.R21R	TCTCCGGGTGCTG	.	342.0	18.0	99.0	0.0	G|0.960;A|0.040	.	Atlas-SNP
MDM2	4193	hgsc.bcm.edu	37	12	69230464	69230464	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MDM2	NM_002392	exon10	c.A853C	p.T285P	CAAGTTACTGTGT	.	149.0	47.0	75.0	0.0	.	.	Atlas-SNP
SCN8A	6334	hgsc.bcm.edu	37	12	52188409	52188409	+	Silent	SNP	C	C	T	rs12301486	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SCN8A	NM_014191	exon26	c.C4779T	p.V1593V	GGTAGTCATCCTC	.	372.0	24.0	113.0	0.0	C|0.992;T|0.008	.	Atlas-SNP
OR6B2	389090	hgsc.bcm.edu	37	2	240969039	240969039	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001005853	exon1	c.T808A	p.S270T	TGTTGGAGCTCTG	.	185.0	58.0	73.0	0.0	.	.	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196786851	196786851	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DNAH7	NM_018897	exon24	c.C3896A	p.P1299H	AGCCTAGGGGAAT	.	284.0	80.0	115.0	0.0	.	.	Atlas-SNP
MIA2	117153	hgsc.bcm.edu	37	14	39722329	39722329	+	Missense_Mutation	SNP	A	A	G	rs61732342	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MIA2	NM_054024	exon6	c.A1841G	p.D614G	TTTATGATTTCAT	.	368.0	17.0	141.0	0.0	A|0.995;G|0.005	.	Atlas-SNP
CHMP1A	5119	hgsc.bcm.edu	37	16	89712997	89712997	+	Nonsense_Mutation	SNP	G	G	A	rs61730918	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001083314	exon5	c.C487T	p.R163X	GCCCTCGGGCAGC	.	140.0	8.0	55.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
CHMP2B	25978	hgsc.bcm.edu	37	3	87302890	87302890	+	Missense_Mutation	SNP	G	G	A	rs78268395	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CHMP2B	NM_014043	exon6	c.G560A	p.S187N	CTCGAAGCTTACC	.	172.0	11.0	63.0	0.0	G|0.993;A|0.007	.	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	37	3	41268766	41268766	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	CTNNB1,NS,Wilms_tumour,0	CTNNB1	NM_001098209	exon7	c.A1004T	p.K335I	ACGAAAAACTACT	.	193.0	61.0	69.0	0.0	.	.	Atlas-SNP
KCTD16	57528	hgsc.bcm.edu	37	5	143853518	143853518	+	Silent	SNP	G	G	A	rs147489800	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KCTD16	NM_020768	exon4	c.G1128A	p.S376S	GGAATCGAACATG	.	236.0	14.0	104.0	0.0	G|0.979;A|0.021	.	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56539199	56539199	+	Missense_Mutation	SNP	A	A	G	rs201311338		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NLRP5	NM_153447	exon7	c.A1600G	p.M534V	TGCCGTATGGCTG	.	261.0	12.0	67.0	0.0	.	.	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232649855	232649855	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SIPA1L2	NM_020808	exon1	c.T1231G	p.Y411D	TAAAGTAAGGACA	.	120.0	42.0	40.0	0.0	.	.	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25312306	25312306	+	Missense_Mutation	SNP	C	C	A	rs73608227	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	THNSL1	NM_024838	exon3	c.C154A	p.L52I	CACTCTCTTGTTG	.	230.0	22.0	126.0	0.0	C|0.982;A|0.018	.	Atlas-SNP
TMEM70	54968	hgsc.bcm.edu	37	8	74893820	74893820	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMEM70	NM_017866	exon3	c.A747C	p.E249D	GGAAGAAACCAGT	.	121.0	15.0	48.0	0.0	.	.	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149506195	149506195	+	Missense_Mutation	SNP	C	C	T	rs73727627	bycluster;byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_198455	exon63	c.C9187T	p.R3063C	AGGAACCGCACCC	.	247.0	16.0	63.0	0.0	C|0.978;T|0.022	.	Atlas-SNP
NRIP1	8204	hgsc.bcm.edu	37	21	16337184	16337184	+	Silent	SNP	A	A	G	rs61733442	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NRIP1	NM_003489	exon4	c.T3330C	p.P1110P	TGCAGTAGGAAGT	.	308.0	14.0	142.0	0.0	A|0.998;G|0.002	.	Atlas-SNP
TMC7	79905	hgsc.bcm.edu	37	16	19051741	19051741	+	Missense_Mutation	SNP	G	G	A	rs73528934	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMC7	NM_024847	exon9	c.G1310A	p.G437D	CTCCAGGCTTTGA	.	97.0	8.0	25.0	0.0	G|0.979;A|0.021	.	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70066424	70066424	+	Missense_Mutation	SNP	T	T	C	rs201914215	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UGT2B11	NM_001073	exon6	c.A1324G	p.I442V	TCATAATATTCTC	.	219.0	11.0	105.0	0.0	T|0.848;C|0.151	.	Atlas-SNP
NFKBIZ	64332	hgsc.bcm.edu	37	3	101572510	101572510	+	Silent	SNP	C	C	T	rs36003810	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NFKBIZ	NM_031419	exon5	c.C1140T	p.S380S	CAGCAGCGCCTGT	.	157.0	9.0	57.0	0.0	C|0.956;T|0.044	.	Atlas-SNP
HK1	3098	hgsc.bcm.edu	37	10	71158513	71158513	+	Silent	SNP	C	C	T	rs10998760	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HK1	NM_033498	exon20	c.C2550T	p.R850R	GATCCGCGAGAAC	.	128.0	13.0	52.0	0.0	C|0.980;T|0.020	.	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179347790	179347790	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AXDND1	NM_144696	exon5	c.C393T	p.Y131Y	TCTGTACGATGTA	.	204.0	12.0	71.0	0.0	.	.	Atlas-SNP
FBXO11	80204	hgsc.bcm.edu	37	2	48066624	48066624	+	Missense_Mutation	SNP	T	T	A	rs17036993	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBXO11	NM_001190274	exon3	c.A376T	p.T126S	CTGTAGTTGAAGT	.	338.0	14.0	104.0	0.0	T|0.974;A|0.026	.	Atlas-SNP
LRIG2	9860	hgsc.bcm.edu	37	1	113657295	113657295	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LRIG2	NM_014813	exon15	c.G2327A	p.R776H	CAGAACGTGGCCA	.	154.0	9.0	46.0	0.0	.	.	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141033823	141033823	+	Missense_Mutation	SNP	C	C	A	rs61746868	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ARAP3	NM_022481	exon33	c.G4329T	p.K1443N	CAATGACTTCTGG	.	309.0	14.0	66.0	0.0	C|0.984;A|0.016	.	Atlas-SNP
BRD9	65980	hgsc.bcm.edu	37	5	886744	886744	+	Missense_Mutation	SNP	C	C	T	rs34292369	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BRD9	NM_023924	exon7	c.G796A	p.A266T	TCTTGGCAGTTTC	.	412.0	18.0	144.0	0.0	C|0.958;T|0.042	.	Atlas-SNP
CEP120	153241	hgsc.bcm.edu	37	5	122718562	122718562	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CEP120	NM_153223	exon14	c.A1882G	p.K628E	ACGGCTTTTGCTG	.	232.0	69.0	132.0	0.0	.	.	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58756075	58756075	+	Silent	SNP	G	G	A	rs75336120	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GOT2	NM_002080	exon3	c.C354T	p.S118S	GACTTCGCTGTTC	.	216.0	11.0	63.0	0.0	G|0.979;A|0.021	.	Atlas-SNP
OR5J2	282775	hgsc.bcm.edu	37	11	55944427	55944427	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5J2	NM_001005492	exon1	c.G334T	p.G112C	ACAGAAGGCTTCT	.	460.0	117.0	168.0	0.0	.	.	Atlas-SNP
CCDC30	728621	hgsc.bcm.edu	37	1	43042767	43042767	+	Missense_Mutation	SNP	A	A	G	rs61729282	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCDC30	NM_001080850	exon7	c.A932G	p.Y311C	CAGAGTACAAGCA	.	113.0	8.0	80.0	0.0	A|0.993;G|0.007	.	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1642698	1642698	+	Missense_Mutation	SNP	G	G	A	rs202081704		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PXDN	NM_012293	exon21	c.C4126T	p.R1376C	CTGAGCGTGTGCT	.	307.0	20.0	71.0	0.0	.	.	Atlas-SNP
CD2AP	23607	hgsc.bcm.edu	37	6	47522408	47522408	+	Silent	SNP	C	C	T	rs145518596	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CD2AP	NM_012120	exon5	c.C447T	p.T149T	TGGAACCCTGAAT	.	395.0	18.0	138.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
FGGY	55277	hgsc.bcm.edu	37	1	59978048	59978048	+	Missense_Mutation	SNP	C	C	G	rs11207463	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FGGY	NM_001113411	exon7	c.C736G	p.L246V	AGAGACCTTGGCC	.	162.0	17.0	46.0	0.0	C|0.985;G|0.015	.	Atlas-SNP
MACC1	346389	hgsc.bcm.edu	37	7	20193822	20193822	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MACC1	NM_182762	exon6	c.T2340C	p.A780A	CTCAACAGCAACA	.	392.0	130.0	153.0	0.0	.	.	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169158470	169158470	+	Missense_Mutation	SNP	G	G	C	rs139699246	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DDX60	NM_017631	exon32	c.C4378G	p.L1460V	GGAAGAGTCCATT	.	206.0	12.0	97.0	0.0	G|0.999;C|0.001	.	Atlas-SNP
OSBPL9	114883	hgsc.bcm.edu	37	1	52251499	52251499	+	Missense_Mutation	SNP	T	T	A	rs149501959	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OSBPL9	NM_148909	exon21	c.T1879A	p.S627T	AAGAAGTCTTTTT	.	145.0	9.0	81.0	0.0	T|0.998;A|0.002	.	Atlas-SNP
EIF2S3	1968	hgsc.bcm.edu	37	X	24078262	24078262	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EIF2S3	NM_001415	exon5	c.C441T	p.N147N	GCTGAACGGTGCA	.	290.0	23.0	76.0	0.0	.	.	Atlas-SNP
SETD3	84193	hgsc.bcm.edu	37	14	99924727	99924727	+	Silent	SNP	G	G	A	rs115281851	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SETD3	NM_032233	exon6	c.C564T	p.Y188Y	TTCAAAGTAGAGA	.	162.0	7.0	82.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
TMEM70	54968	hgsc.bcm.edu	37	8	74893799	74893799	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMEM70	NM_017866	exon3	c.A726G	p.E242E	AGAAGAATTTATT	.	185.0	20.0	59.0	0.0	.	.	Atlas-SNP
USP24	23358	hgsc.bcm.edu	37	1	55620128	55620128	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USP24	NM_015306	exon14	c.T1566C	p.T522T	ACTCTCAGTCTCC	.	115.0	24.0	68.0	0.0	.	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228452066	228452066	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OBSCN	NM_001271223	exon18	c.G5387A	p.R1796Q	ATCAGCGGCTGTC	.	248.0	10.0	129.0	0.0	.	.	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205898421	205898421	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC26A9	NM_134325	exon7	c.A781C	p.I261L	CGCTGATGAGAGC	.	156.0	12.0	47.0	0.0	.	.	Atlas-SNP
CEBPE	1053	hgsc.bcm.edu	37	14	23586714	23586714	+	Silent	SNP	G	G	A	rs143753215	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CEBPE	NM_001805	exon2	c.C828T	p.G276G	CCCCACGCCCTTG	.	96.0	6.0	26.0	0.0	G|1.000;A|0.000	.	Atlas-SNP
AKAP3	10566	hgsc.bcm.edu	37	12	4735801	4735801	+	Missense_Mutation	SNP	G	G	T	rs115289691	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AKAP3	NM_006422	exon4	c.C2267A	p.T756K	ATCACCGTGGGTG	.	336.0	16.0	167.0	0.0	G|0.993;T|0.007	.	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	40062748	40062748	+	Missense_Mutation	SNP	T	T	C	rs1166719	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FSIP1	NM_152597	exon3	c.A190G	p.N64D	TTCTGTTCTCTGT	.	386.0	20.0	175.0	0.0	T|0.991;C|0.009	.	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	37	4	30724235	30724235	+	Silent	SNP	C	C	T	rs35941707	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDH7	NM_032457	exon1	c.C1191T	p.D397D	GACCGACAAGGCC	.	140.0	16.0	70.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
TAOK1	57551	hgsc.bcm.edu	37	17	27802783	27802783	+	Silent	SNP	A	A	G	rs147203802	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TAOK1	NM_025142	exon4	c.A300G	p.T100T	ACACACAGCATGG	.	333.0	17.0	111.0	0.0	A|0.998;G|0.002	.	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	37	4	56770509	56770509	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EXOC1	NM_018261	exon19	c.G2533A	p.V845M	TAATAGGTGGTGT	.	135.0	37.0	71.0	0.0	.	.	Atlas-SNP
NAT6	24142	hgsc.bcm.edu	37	3	50334099	50334099	+	Silent	SNP	G	G	A	rs192428304		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NAT6	NM_012191	exon2	c.C862T	p.L288L	CCAGCAGGCTTTT	.	221.0	14.0	97.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115956400	115956400	+	Missense_Mutation	SNP	C	C	T	rs62636616	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FKBP15	NM_015258	exon10	c.G914A	p.R305H	GAATCGCGGGAAC	.	105.0	10.0	59.0	0.0	C|0.990;T|0.010	.	Atlas-SNP
GAS2L2	246176	hgsc.bcm.edu	37	17	34072245	34072245	+	Silent	SNP	C	C	T	rs114664198	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GAS2L2	NM_139285	exon6	c.G2271A	p.K757K	CCTGCCCTTGCTC	.	229.0	12.0	66.0	0.0	C|0.991;T|0.009	.	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11419287	11419287	+	Silent	SNP	C	C	T	rs17164530	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	THSD7A	NM_015204	exon24	c.G4560A	p.P1520P	ACTACACGGTGGG	.	158.0	10.0	73.0	0.0	C|0.987;T|0.013	.	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	37	1	87043670	87043670	+	Silent	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CLCA4	NM_012128	exon12	c.G2037T	p.R679R	AGTTCGGGCTCAT	.	172.0	31.0	116.0	0.0	.	.	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72132927	72132927	+	Missense_Mutation	SNP	G	G	T	rs143671341	byfrequency;alternate_allele	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DHX38	NM_014003	exon6	c.G866T	p.R289L	CCCCGCGTCTGTC	.	61.0	18.0	30.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
TSR1	55720	hgsc.bcm.edu	37	17	2233869	2233869	+	Silent	SNP	G	G	A	rs111973646	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TSR1	NM_018128	exon10	c.C1710T	p.V570V	GCACTCGACCACT	.	185.0	11.0	79.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
H6PD	9563	hgsc.bcm.edu	37	1	9307075	9307075	+	Silent	SNP	C	C	T	rs36094664	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	H6PD	NM_004285	exon3	c.C678T	p.D226D	TTTGGACGGCCTC	.	115.0	8.0	37.0	0.0	C|0.991;T|0.009	.	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7717314	7717314	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADCY2	NM_020546	exon12	c.G1667A	p.R556K	ATGAAAGGATGAT	.	882.0	304.0	369.0	0.0	.	.	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81572097	81572097	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IL16	NM_001172128	exon8	c.G1063T	p.E355X	ATGGTGGAGGTTT	.	120.0	31.0	47.0	0.0	.	.	Atlas-SNP
REEP3	221035	hgsc.bcm.edu	37	10	65354554	65354554	+	Missense_Mutation	SNP	A	A	T	rs200806624		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001001330	exon3	c.A122T	p.Y41F	TGATGTACTGGAT	.	585.0	24.0	174.0	0.0	.	.	Atlas-SNP
SEMG2	6407	hgsc.bcm.edu	37	20	43851922	43851922	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SEMG2	NM_003008	exon2	c.C1649G	p.S550C	AGGAATCCAGTGA	.	258.0	25.0	140.0	0.0	.	.	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32944667	32944667	+	Silent	SNP	A	A	C	rs9590940	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BRCA2	NM_000059	exon19	c.A8460C	p.V2820V	TGATGTAATTATT	.	485.0	20.0	195.0	0.0	A|0.988;C|0.012	.	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57328213	57328213	+	Missense_Mutation	SNP	C	C	A	rs28524173	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PEG3	NM_001146184	exon9	c.G1597T	p.V533L	ATTCCACAAGATA	.	191.0	12.0	89.0	0.0	C|0.986;A|0.014	.	Atlas-SNP
PIGX	54965	hgsc.bcm.edu	37	3	196454936	196454936	+	Missense_Mutation	SNP	G	G	A	rs150787833	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PIGX	NM_017861	exon4	c.G461A	p.R154Q	ATCATCGGCCGCA	.	301.0	22.0	141.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983173	97983173	+	Silent	SNP	G	G	A	rs74600825	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5H6	NM_001005479	exon1	c.G45A	p.E15E	CAGTGAGGAGATG	.	347.0	14.0	145.0	0.0	G|0.977;A|0.023	.	Atlas-SNP
ALG8	79053	hgsc.bcm.edu	37	11	77823732	77823732	+	Silent	SNP	A	A	G	rs61995924	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ALG8	NM_024079	exon8	c.T862C	p.L288L	TGTACAAAGCCCA	.	116.0	12.0	59.0	0.0	A|0.954;G|0.046	.	Atlas-SNP
PSG7	5676	hgsc.bcm.edu	37	19	43430126	43430126	+	Missense_Mutation	SNP	G	G	C	rs147075594		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001206650	exon4	c.C676G	p.Q226E	GGTTTTGTCCTGA	.	231.0	12.0	90.0	0.0	G|0.997;C|0.003	.	Atlas-SNP
SYCP1	6847	hgsc.bcm.edu	37	1	115527364	115527364	+	Missense_Mutation	SNP	C	C	T	rs150731809	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SYCP1	NM_003176	exon30	c.C2578T	p.P860S	AAGACACCAACAA	.	488.0	24.0	236.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
LYST	1130	hgsc.bcm.edu	37	1	235920740	235920740	+	Silent	SNP	C	C	T	rs10926586	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LYST	NM_000081	exon24	c.G6900A	p.L2300L	AGGTACCAAACAG	.	279.0	13.0	116.0	0.0	C|0.971;T|0.029	.	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152496908	152496908	+	Silent	SNP	G	G	A	rs61730773		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NEB	NM_004543	exon61	c.C8646T	p.D2882D	GATGACGTCGCTC	.	350.0	17.0	108.0	0.0	G|0.987;A|0.013	.	Atlas-SNP
ZW10	9183	hgsc.bcm.edu	37	11	113607488	113607488	+	Silent	SNP	A	A	G	rs146501766	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZW10	NM_004724	exon15	c.T2073C	p.D691D	TCCTTCATCCATC	.	402.0	20.0	149.0	0.0	A|0.998;G|0.002	.	Atlas-SNP
MC2R	4158	hgsc.bcm.edu	37	18	13885109	13885109	+	Missense_Mutation	SNP	G	G	A	rs104894660	bycluster	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MC2R	NM_000529	exon2	c.C409T	p.R137W	GGTACCGCAGTGC	.	58.0	26.0	27.0	0.0	.	.	Atlas-SNP
CXorf65	158830	hgsc.bcm.edu	37	X	70325963	70325963	+	Missense_Mutation	SNP	G	G	A	rs138480889	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CXorf65	NM_001025265	exon3	c.C137T	p.T46M	TTCCCCGTTTGTT	.	84.0	10.0	24.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
HLCS	3141	hgsc.bcm.edu	37	21	38309184	38309184	+	Silent	SNP	G	G	A	rs116114362	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HLCS	NM_000411	exon5	c.C561T	p.A187A	ACAGTCGGCCAGC	.	138.0	6.0	52.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
MEPE	56955	hgsc.bcm.edu	37	4	88766686	88766686	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MEPE	NM_020203	exon4	c.C666T	p.Y222Y	TGACTACCTAAAA	.	102.0	30.0	47.0	0.0	.	.	Atlas-SNP
AQP9	366	hgsc.bcm.edu	37	15	58467196	58467196	+	Silent	SNP	A	A	T	rs140188159	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AQP9	NM_020980	exon4	c.A456T	p.P152P	ATACCCAGCTCCG	.	204.0	11.0	88.0	0.0	A|0.998;T|0.002	.	Atlas-SNP
ISLR	3671	hgsc.bcm.edu	37	15	74468009	74468009	+	Silent	SNP	C	C	T	rs115861726	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ISLR	NM_201526	exon2	c.C810T	p.H270H	CTGGCACATCCAG	.	189.0	10.0	46.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	37	12	89916665	89916665	+	Silent	SNP	C	C	T	rs7299750	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_003774	exon1	c.G1662A	p.P554P	GCCCTCCGGTGTC	.	279.0	14.0	135.0	0.0	C|0.988;T|0.012	.	Atlas-SNP
CCDC77	84318	hgsc.bcm.edu	37	12	527792	527792	+	Silent	SNP	C	C	T	rs147266504	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCDC77	NM_032358	exon5	c.C403T	p.L135L	GACCGACTGAGAA	.	170.0	14.0	61.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
PTGES3	10728	hgsc.bcm.edu	37	12	57066778	57066778	+	Missense_Mutation	SNP	T	T	C	rs141815775	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PTGES3	NM_006601	exon2	c.A74G	p.K25R	ACATCCTTACTGT	.	264.0	11.0	104.0	0.0	T|0.997;C|0.003	.	Atlas-SNP
C11orf35	256329	hgsc.bcm.edu	37	11	557444	557444	+	Missense_Mutation	SNP	C	C	T	rs61329792	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C11orf35	NM_173573	exon7	c.G668A	p.R223Q	GGATACCGGCGGG	.	183.0	10.0	65.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
GIMAP8	155038	hgsc.bcm.edu	37	7	150164189	150164189	+	Silent	SNP	C	C	A	rs143212982	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GIMAP8	NM_175571	exon2	c.C403A	p.R135R	TTCACTCGGAAGG	.	196.0	8.0	72.0	0.0	A|0.002;C|0.998;G|0.001	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228481947	228481947	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OBSCN	NM_001271223	exon47	c.G12513A	p.P4171P	GGCACCGGTGGAG	.	277.0	14.0	116.0	0.0	.	.	Atlas-SNP
ANO10	55129	hgsc.bcm.edu	37	3	43602810	43602810	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ANO10	NM_018075	exon9	c.G1378A	p.G460S	GCACACCATGCTT	.	307.0	14.0	136.0	0.0	.	.	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39846038	39846038	+	Silent	SNP	A	A	G	rs6673570	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MACF1	NM_012090	exon51	c.A7455G	p.E2485E	TCAGGAAGAACTC	.	143.0	12.0	83.0	0.0	A|0.986;G|0.014	.	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222712078	222712078	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HHIPL2	NM_024746	exon5	c.G1489A	p.G497R	ACTTCCCCACTGC	.	219.0	70.0	77.0	0.0	.	.	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135204769	135204769	+	Missense_Mutation	SNP	C	C	T	rs36024203	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SETX	NM_015046	exon10	c.G2216A	p.G739E	ATTATTCCTCTGT	.	183.0	8.0	128.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98220464	98220464	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PTCH1	NM_000264	exon18	c.A2999G	p.N1000S	GTATAGTTGCTGC	.	187.0	78.0	99.0	0.0	.	.	Atlas-SNP
NAP1L2	4674	hgsc.bcm.edu	37	X	72434302	72434302	+	Silent	SNP	C	C	T	rs34495238	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NAP1L2	NM_021963	exon1	c.G27A	p.E9E	TGACAGCTCCTTG	.	121.0	11.0	43.0	0.0	C|0.970;T|0.030	.	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204217949	204217949	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLEKHA6	NM_014935	exon12	c.G1824T	p.T608T	GGTTACCGTGGTC	.	111.0	46.0	35.0	0.0	.	.	Atlas-SNP
PPEF1	5475	hgsc.bcm.edu	37	X	18802154	18802154	+	Silent	SNP	A	A	G	rs61731650	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPEF1	NM_152226	exon12	c.A900G	p.V300V	CCGTGTAGAGAGG	.	191.0	15.0	79.0	0.0	A|0.983;G|0.017	.	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166848462	166848462	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SCN1A	NM_001165963	exon26	c.C5323A	p.L1775M	CAACCAGGAAGGA	.	390.0	118.0	140.0	0.0	.	.	Atlas-SNP
SLCO1B7	338821	hgsc.bcm.edu	37	12	21243035	21243035	+	Missense_Mutation	SNP	C	C	A	rs73241802		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001009562	exon13	c.C1918A	p.Q640K	GAAGAACAGTAAA	.	187.0	12.0	96.0	0.0	C|0.980;A|0.020	.	Atlas-SNP
PDE6C	5146	hgsc.bcm.edu	37	10	95418883	95418883	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PDE6C	NM_006204	exon18	c.G2167C	p.D723H	GCATGTGACTTGT	.	315.0	102.0	105.0	0.0	.	.	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	37	5	156757852	156757852	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CYFIP2	NM_001037332	exon20	c.C2259T	p.H753H	GAGACACGTCCAG	.	155.0	56.0	105.0	0.0	.	.	Atlas-SNP
VPS13D	55187	hgsc.bcm.edu	37	1	12304644	12304644	+	Silent	SNP	C	C	T	rs34489138	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	VPS13D	NM_015378	exon5	c.C417T	p.S139S	CGCCTCCGTAGTT	.	182.0	9.0	97.0	0.0	C|0.994;T|0.006	.	Atlas-SNP
CYYR1	116159	hgsc.bcm.edu	37	21	27852641	27852641	+	Missense_Mutation	SNP	C	C	T	rs35253087	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CYYR1	NM_052954	exon3	c.G284A	p.R95H	CCCACGCGGGTCG	.	133.0	8.0	45.0	0.0	C|0.976;T|0.024	.	Atlas-SNP
SLC6A18	348932	hgsc.bcm.edu	37	5	1244871	1244871	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC6A18	NM_182632	exon11	c.A1645G	p.N549D	GCCTGGAACCCCA	.	113.0	25.0	31.0	0.0	.	.	Atlas-SNP
USP14	9097	hgsc.bcm.edu	37	18	180336	180336	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USP14	NM_005151	exon5	c.A401G	p.K134R	CCCTTAAAAGGTA	.	99.0	37.0	45.0	0.0	.	.	Atlas-SNP
OR4K13	390433	hgsc.bcm.edu	37	14	20502779	20502779	+	Missense_Mutation	SNP	C	C	T	rs144683363	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR4K13	NM_001004714	exon1	c.G139A	p.V47M	CAGTCACCAAGAT	.	216.0	10.0	82.0	0.0	C|0.985;T|0.015	.	Atlas-SNP
CC2D1B	200014	hgsc.bcm.edu	37	1	52826157	52826157	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CC2D1B	NM_032449	exon6	c.C542T	p.A181V	CTGGCCGCAGCCT	.	115.0	10.0	55.0	0.0	.	.	Atlas-SNP
PRPH	5630	hgsc.bcm.edu	37	12	49689157	49689157	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRPH	NM_006262	exon1	c.C174A	p.G58G	CCTGGGCAGCTTC	.	57.0	16.0	22.0	0.0	.	.	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140257289	140257289	+	Silent	SNP	C	C	T	rs116613760	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_018903	exon1	c.C2232T	p.A744A	CAGCGCCGTGGGG	.	203.0	12.0	80.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
CACNB2	783	hgsc.bcm.edu	37	10	18828455	18828455	+	Silent	SNP	C	C	T	rs61733967	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CACNB2	NM_201596	exon14	c.C1785T	p.H595H	GACCCACGGGAGC	.	122.0	7.0	71.0	0.0	C|0.988;T|0.012	.	Atlas-SNP
SURF4	6836	hgsc.bcm.edu	37	9	136230610	136230610	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SURF4	NM_033161	exon6	c.C569G	p.A190G	ATCAGAGCTGTGC	.	70.0	23.0	34.0	0.0	.	.	Atlas-SNP
ATP6V1E2	90423	hgsc.bcm.edu	37	2	46739683	46739683	+	Silent	SNP	A	A	G	rs17035245	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATP6V1E2	NM_080653	exon2	c.T168C	p.Y56Y	CTCATAATACTCC	.	472.0	19.0	110.0	0.0	A|0.964;G|0.036	.	Atlas-SNP
FBXL18	80028	hgsc.bcm.edu	37	7	5540245	5540245	+	Missense_Mutation	SNP	T	T	C	rs74478333		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBXL18	NM_024963	exon3	c.A1655G	p.N552S	CCGATATTGACCA	.	77.0	8.0	28.0	0.0	T|0.983;C|0.017	.	Atlas-SNP
KARS	3735	hgsc.bcm.edu	37	16	75662488	75662488	+	Silent	SNP	G	G	A	rs143267922	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KARS	NM_001130089	exon14	c.C1758T	p.L586L	GTCCGTGAGAAAC	.	245.0	17.0	85.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
USP54	159195	hgsc.bcm.edu	37	10	75277310	75277310	+	Silent	SNP	C	C	A	rs144319515		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USP54	NM_152586	exon18	c.G2874T	p.S958S	TTCAACCGAAGTC	.	315.0	14.0	116.0	0.0	C|0.999;A|0.001	.	Atlas-SNP
PLAT	5327	hgsc.bcm.edu	37	8	42033519	42033519	+	Nonsense_Mutation	SNP	G	G	A	rs1804182	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLAT	NM_000930	exon14	c.C1681T	p.R561X	ACGGTCGCATGTT	.	229.0	14.0	134.0	0.0	G|0.992;A|0.008	.	Atlas-SNP
RHD	6007	hgsc.bcm.edu	37	1	25627559	25627559	+	Silent	SNP	G	G	A	rs114032679	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RHD	NM_001127691	exon4	c.G609A	p.T203T	AGCAACGATACCC	.	12.0	12.0	2.0	0.0	G|0.981;A|0.019	.	Atlas-SNP
CLIP1	6249	hgsc.bcm.edu	37	12	122825734	122825734	+	Missense_Mutation	SNP	C	C	T	rs201352592		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CLIP1	NM_001247997	exon11	c.G2017A	p.E673K	CTATTTCGTGTTG	.	549.0	25.0	278.0	0.0	C|0.999;T|0.000	.	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32630282	32630282	+	Missense_Mutation	SNP	T	T	C	rs61736667	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TAF1L	NM_153809	exon1	c.A5296G	p.I1766V	CAGATATAAGCAA	.	424.0	23.0	220.0	0.0	T|0.988;C|0.012	.	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89836575	89836575	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FANCA	NM_000135	exon25	c.A2315G	p.Q772R	CTCACCTGGTGAC	.	37.0	17.0	12.0	0.0	.	.	Atlas-SNP
KIAA1804	0	hgsc.bcm.edu	37	1	233512273	233512273	+	Missense_Mutation	SNP	G	G	A	rs138394059	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIAA1804	NM_032435	exon8	c.G1924A	p.G642R	CAGCCAGGTAAAT	.	225.0	20.0	84.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
TMEM201	199953	hgsc.bcm.edu	37	1	9661189	9661189	+	Silent	SNP	G	G	A	rs141781360	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMEM201	NM_001010866	exon5	c.G633A	p.P211P	GTCCCCGGTCCAG	.	250.0	12.0	75.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
NCOA6	23054	hgsc.bcm.edu	37	20	33338099	33338099	+	Silent	SNP	G	G	A	rs61736335	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NCOA6	NM_014071	exon9	c.C1899T	p.G633G	CATCTGGCCCTGG	.	175.0	13.0	37.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
TBC1D8B	54885	hgsc.bcm.edu	37	X	106083331	106083331	+	Silent	SNP	A	A	G	rs73531168	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TBC1D8B	NM_198881	exon9	c.A1407G	p.G469G	ATGTGGACGTGGT	.	379.0	19.0	153.0	0.0	A|0.917;G|0.083	.	Atlas-SNP
WNK3	65267	hgsc.bcm.edu	37	X	54263455	54263455	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WNK3	NM_020922	exon20	c.C4544T	p.S1515L	GATGGCGAATAGA	.	241.0	15.0	76.0	0.0	.	.	Atlas-SNP
ZNF211	10520	hgsc.bcm.edu	37	19	58152182	58152182	+	Missense_Mutation	SNP	G	G	A	rs34897843	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF211	NM_001265597	exon5	c.G523A	p.D175N	AATGCCGACTCCT	.	332.0	21.0	108.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156926617	156926617	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADAM19	NM_033274	exon13	c.G1362A	p.A454A	ACACTCCGCCCCC	.	250.0	17.0	95.0	0.0	.	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113392672	113392672	+	Silent	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CSMD3	NM_198123	exon38	c.C6045G	p.P2015P	AAGATGGGGTATT	.	184.0	107.0	31.0	0.0	.	.	Atlas-SNP
GTF3C2	2976	hgsc.bcm.edu	37	2	27564998	27564998	+	Silent	SNP	C	C	T	rs77603674	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GTF3C2	NM_001521	exon5	c.T672A	p.G224G	CTTCTTCGGTTTG	.	200.0	10.0	42.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
JHDM1D	80853	hgsc.bcm.edu	37	7	139797347	139797347	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	JHDM1D	NM_030647	exon15	c.C2014T	p.L672L	GTACCAGTGCAGT	.	188.0	79.0	42.0	0.0	.	.	Atlas-SNP
SPINT3	10816	hgsc.bcm.edu	37	20	44141410	44141410	+	Nonsense_Mutation	SNP	G	G	A	rs148191315	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_006652	exon2	c.C151T	p.R51X	ACCATCGCGTCAT	.	104.0	10.0	46.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88780150	88780150	+	Silent	SNP	C	C	T	rs2340974	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CTU2	NM_001012759	exon9	c.C969T	p.S323S	GTTCTCCGTTCCT	.	90.0	5.0	42.0	0.0	C|0.985;T|0.015	.	Atlas-SNP
PPM1M	132160	hgsc.bcm.edu	37	3	52281703	52281703	+	Silent	SNP	G	G	A	rs115706924	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_144641	exon4	c.G603A	p.E201E	GGATGAGGTGATC	.	121.0	5.0	54.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
RALGAPA2	57186	hgsc.bcm.edu	37	20	20618108	20618108	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RALGAPA2	NM_020343	exon8	c.A704T	p.D235V	CCAGTATCTTGAT	.	261.0	11.0	171.0	0.0	.	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228464309	228464309	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OBSCN	NM_001271223	exon26	c.C7504A	p.R2502R	GCTGTGCGGGGCC	.	246.0	76.0	82.0	0.0	.	.	Atlas-SNP
CDCP1	64866	hgsc.bcm.edu	37	3	45153778	45153778	+	Missense_Mutation	SNP	G	G	A	rs144845427		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CDCP1	NM_178181	exon3	c.C452T	p.P151L	TCACCCGGACCGA	.	153.0	10.0	62.0	0.0	G|1.000;A|0.000	.	Atlas-SNP
PIK3CA	5290	hgsc.bcm.edu	37	3	178927410	178927410	+	Missense_Mutation	SNP	A	A	G	rs3729680	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PIK3CA	NM_006218	exon7	c.A1173G	p.I391M	TGATATATACATT	.	470.0	34.0	169.0	0.0	A|0.924;G|0.076	.	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3227934	3227934	+	Silent	SNP	C	C	T	rs137855629	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MXRA5	NM_015419	exon7	c.G8310A	p.P2770P	CTTATCCGGTAAC	.	227.0	21.0	91.0	0.0	C|0.960;T|0.040	.	Atlas-SNP
ZHX3	23051	hgsc.bcm.edu	37	20	39833003	39833003	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZHX3	NM_015035	exon3	c.C554A	p.P185Q	ATGATTGGAGTTT	.	244.0	77.0	110.0	0.0	.	.	Atlas-SNP
IL27RA	9466	hgsc.bcm.edu	37	19	14153567	14153567	+	Missense_Mutation	SNP	C	C	T	rs149346880	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IL27RA	NM_004843	exon6	c.C734T	p.T245M	GTGGGACGCCTGG	.	412.0	17.0	132.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205892228	205892228	+	Silent	SNP	A	A	G	rs140575203	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC26A9	NM_134325	exon16	c.T1755C	p.S585S	GAATAGAGACCTC	.	581.0	26.0	140.0	0.0	A|0.993;G|0.007	.	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26535844	26535844	+	Silent	SNP	C	C	T	rs75113578	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GPR113	NM_001145168	exon10	c.G1620A	p.E540E	TCTGGCCTCTGCC	.	140.0	9.0	46.0	0.0	C|0.978;T|0.022	.	Atlas-SNP
PPP4R2	151987	hgsc.bcm.edu	37	3	73114696	73114696	+	Silent	SNP	A	A	G	rs142951081	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPP4R2	NM_174907	exon9	c.A1077G	p.L359L	TTTGCTACATTCT	.	437.0	21.0	210.0	0.0	A|0.997;G|0.003	.	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98545948	98545948	+	Silent	SNP	G	G	T	rs35426979	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRRAP	NM_001244580	exon33	c.G4632T	p.R1544R	GGAGCGGGCGATG	.	120.0	6.0	48.0	0.0	G|0.992;T|0.008	.	Atlas-SNP
N4BP2L2	10443	hgsc.bcm.edu	37	13	33101574	33101574	+	Missense_Mutation	SNP	C	C	T	rs149866043	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	N4BP2L2	NM_014887	exon3	c.G1355A	p.G452D	GCATCACCAAGTT	.	119.0	10.0	29.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
HIST3H3	8290	hgsc.bcm.edu	37	1	228612760	228612760	+	Silent	SNP	G	G	A	rs143686240	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HIST3H3	NM_003493	exon1	c.C267T	p.A89A	CATCACGGCCGAG	.	153.0	7.0	54.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	37	1	32256329	32256329	+	Missense_Mutation	SNP	G	G	A	rs36047547	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SPOCD1	NM_144569	exon16	c.C3526T	p.P1176S	GGCGGGGGATGGA	.	127.0	11.0	32.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
CYBA	1535	hgsc.bcm.edu	37	16	88713224	88713224	+	Missense_Mutation	SNP	C	C	T	rs149344911	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CYBA	NM_000101	exon4	c.G226A	p.V76M	TCACCACGGCGGT	.	39.0	7.0	21.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
PPP1R36	145376	hgsc.bcm.edu	37	14	65032134	65032134	+	Missense_Mutation	SNP	G	G	A	rs139652811	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_172365	exon5	c.G329A	p.R110Q	AGAAACGAGGTCA	.	344.0	16.0	138.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43614395	43614395	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SCUBE1	NM_173050	exon15	c.G1757C	p.R586P	GACTTGCGCAGGG	.	81.0	22.0	30.0	0.0	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179431170	179431170	+	Silent	SNP	G	G	T	rs10185798	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TTN	NM_001267550	exon326	c.C79689A	p.V26563V	GGCACAGACTCGT	.	174.0	10.0	56.0	0.0	G|0.993;T|0.007	.	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149506160	149506160	+	Missense_Mutation	SNP	C	C	T	rs139270844		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_198455	exon63	c.C9152T	p.P3051L	GGTCTCCGTGCTC	.	198.0	11.0	55.0	0.0	C|0.994;T|0.006	.	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	37	19	50099235	50099235	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRR12	NM_020719	exon4	c.G1643T	p.W548L	GTGGCTGGGGACC	.	31.0	11.0	12.0	0.0	.	.	Atlas-SNP
SETD3	84193	hgsc.bcm.edu	37	14	99932071	99932071	+	Silent	SNP	T	T	C	rs34435718	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SETD3	NM_032233	exon2	c.A72G	p.E24E	CAAGATTTCCTTT	.	313.0	15.0	102.0	0.0	T|0.991;C|0.009	.	Atlas-SNP
EXOSC9	5393	hgsc.bcm.edu	37	4	122738009	122738009	+	Missense_Mutation	SNP	T	T	G	rs143634561		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EXOSC9	NM_001034194	exon13	c.T1369G	p.X457E	GCCAATTAAAGCT	.	345.0	20.0	182.0	0.0	T|1.000;G|0.000	.	Atlas-SNP
SAMD13	148418	hgsc.bcm.edu	37	1	84791363	84791363	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SAMD13	NM_001010971	exon3	c.G139T	p.V47L	TGGGCCGTGATGG	.	239.0	75.0	95.0	0.0	.	.	Atlas-SNP
DCLK1	9201	hgsc.bcm.edu	37	13	36699915	36699915	+	Silent	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DCLK1	NM_004734	exon2	c.G360C	p.L120L	TTGGTCCAGGCTG	.	52.0	21.0	22.0	0.0	.	.	Atlas-SNP
TMEM39B	55116	hgsc.bcm.edu	37	1	32560397	32560397	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMEM39B	NM_018056	exon7	c.T940C	p.Y314H	CATTACTATGACA	.	220.0	93.0	82.0	0.0	.	.	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124358381	124358381	+	Silent	SNP	C	C	T	rs139554705		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DMBT1	NM_007329	exon26	c.C3048T	p.T1016T	GGGCACCGTGTGC	.	107.0	5.0	40.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
CNKSR2	22866	hgsc.bcm.edu	37	X	21488889	21488889	+	Silent	SNP	T	T	C	rs34161348	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CNKSR2	NM_001168647	exon5	c.T525C	p.C175C	GGATTGTACTGTA	.	483.0	29.0	135.0	0.0	T|0.988;C|0.012	.	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61513135	61513135	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DIDO1	NM_001193369	exon16	c.C4173T	p.Y1391Y	CGGGTCGTACTCC	.	116.0	7.0	45.0	0.0	.	.	Atlas-SNP
SEPT14	346288	hgsc.bcm.edu	37	7	55910750	55910750	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_207366	exon5	c.G443A	p.R148H	AAGGAACGTTTAA	.	193.0	9.0	70.0	0.0	.	.	Atlas-SNP
EEF1A1	1915	hgsc.bcm.edu	37	6	74229680	74229680	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EEF1A1	NM_001402	exon2	c.A70G	p.T24A	GGCCAGTAGTGGT	.	69.0	26.0	17.0	0.0	.	.	Atlas-SNP
PRDM7	11105	hgsc.bcm.edu	37	16	90141351	90141351	+	Missense_Mutation	SNP	C	C	T	rs201333672		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRDM7	NM_001098173	exon3	c.G274A	p.D92N	CTTCATCGGAATC	.	388.0	20.0	199.0	0.0	C|0.999;T|0.000	.	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6302959	6302959	+	Silent	SNP	C	C	T	rs141218500		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MCPH1	NM_001172574	exon8	c.C1716T	p.N572N	ATCAAACTCCTCT	.	86.0	6.0	86.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
PIWIL2	55124	hgsc.bcm.edu	37	8	22147755	22147755	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PIWIL2	NM_001135721	exon10	c.C1077A	p.I359I	GCAGATCTGGCCA	.	191.0	16.0	89.0	0.0	.	.	Atlas-SNP
OR4C6	219432	hgsc.bcm.edu	37	11	55432933	55432933	+	Silent	SNP	C	C	T	rs77687368	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR4C6	NM_001004704	exon1	c.C291T	p.T97T	CCTCACCCAGCTG	.	603.0	29.0	191.0	0.0	C|0.994;T|0.006	.	Atlas-SNP
CPA3	1359	hgsc.bcm.edu	37	3	148599357	148599357	+	Silent	SNP	C	C	A	rs141357361	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CPA3	NM_001870	exon7	c.C625A	p.R209R	TTGGACCGAATGA	.	127.0	8.0	46.0	0.0	C|0.997;A|0.003	.	Atlas-SNP
PSEN1	5663	hgsc.bcm.edu	37	14	73637738	73637738	+	Silent	SNP	C	C	G	rs139863395	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PSEN1	NM_000021	exon4	c.C321G	p.T107T	TTATACCCGGAAG	.	382.0	20.0	172.0	0.0	C|0.999;G|0.001	.	Atlas-SNP
MRPL46	26589	hgsc.bcm.edu	37	15	89010407	89010407	+	Missense_Mutation	SNP	C	C	T	rs147896985	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MRPL46	NM_022163	exon1	c.G202A	p.E68K	TCTCTTCCTGCAA	.	171.0	7.0	55.0	0.0	C|0.987;T|0.013	.	Atlas-SNP
PPP1R13B	23368	hgsc.bcm.edu	37	14	104206784	104206784	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPP1R13B	NM_015316	exon12	c.C1969T	p.P657S	CTGCGGGGGCGGC	.	171.0	8.0	41.0	0.0	.	.	Atlas-SNP
ERN1	2081	hgsc.bcm.edu	37	17	62157052	62157052	+	Silent	SNP	C	C	T	rs113446786		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ERN1	NM_001433	exon4	c.G252A	p.T84T	TCCAAGCGTATAC	.	286.0	12.0	160.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
ACVR1C	130399	hgsc.bcm.edu	37	2	158406777	158406777	+	Silent	SNP	G	G	A	rs115029463	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ACVR1C	NM_145259	exon4	c.C672T	p.F224F	GGAGGAGAATATT	.	394.0	29.0	128.0	0.0	G|0.993;A|0.007	.	Atlas-SNP
PSKH2	85481	hgsc.bcm.edu	37	8	87060743	87060743	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PSKH2	NM_033126	exon3	c.G1106A	p.W369X	TTGCTCCACATAT	.	228.0	30.0	46.0	0.0	.	.	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	37	17	74288596	74288596	+	Missense_Mutation	SNP	G	G	A	rs147284874	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	QRICH2	NM_032134	exon4	c.C1714T	p.R572C	AACCACGCTGATC	.	170.0	10.0	51.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
ZNF385D	79750	hgsc.bcm.edu	37	3	21706469	21706469	+	Missense_Mutation	SNP	G	G	T	rs114302168	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF385D	NM_024697	exon2	c.C74A	p.P25H	AAAGGAGGGGCTG	.	137.0	8.0	49.0	0.0	G|0.973;T|0.027	.	Atlas-SNP
WWP1	11059	hgsc.bcm.edu	37	8	87473479	87473479	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WWP1	NM_007013	exon23	c.A2526G	p.V842V	TGAAGTAAGAATG	.	346.0	61.0	86.0	0.0	.	.	Atlas-SNP
CTSE	1510	hgsc.bcm.edu	37	1	206327553	206327553	+	Missense_Mutation	SNP	G	G	T	rs61742549	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CTSE	NM_001910	exon6	c.G742T	p.V248F	AATTGGGTCCCAG	.	253.0	14.0	53.0	0.0	G|0.997;T|0.003	.	Atlas-SNP
ARSF	416	hgsc.bcm.edu	37	X	3019246	3019246	+	Missense_Mutation	SNP	G	G	T	rs140413167	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ARSF	NM_004042	exon8	c.G1086T	p.W362C	TGGATGGAATGGA	.	173.0	8.0	70.0	0.0	G|0.999;T|0.001	.	Atlas-SNP
CDK17	5128	hgsc.bcm.edu	37	12	96679853	96679853	+	Silent	SNP	A	A	G	rs146214342	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CDK17	NM_001170464	exon13	c.T1290C	p.Y430Y	TGGTTTATATTTT	.	409.0	22.0	162.0	0.0	A|0.996;G|0.004	.	Atlas-SNP
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390069	93390069	+	Missense_Mutation	SNP	A	A	G	rs143318107	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPP1R3C	NM_005398	exon2	c.T569C	p.F190S	GAATCGAAAGTGA	.	126.0	8.0	59.0	0.0	A|0.996;G|0.004	.	Atlas-SNP
MLLT6	4302	hgsc.bcm.edu	37	17	36876805	36876805	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MLLT6	NM_005937	exon15	c.A2336G	p.Y779C	GGCCCTATGGCCT	.	68.0	26.0	36.0	0.0	.	.	Atlas-SNP
PRKAR1B	5575	hgsc.bcm.edu	37	7	635834	635834	+	Silent	SNP	C	C	T	rs79302454	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRKAR1B	NM_001164760	exon7	c.G657A	p.T219T	GAGGTCCGTCTTG	.	103.0	8.0	36.0	0.0	C|0.995;T|0.005	.	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103468870	103468870	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001204425	exon2	c.A571G	p.I191V	GAAGATATTAAAC	.	217.0	67.0	104.0	0.0	.	.	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416296	105416296	+	Missense_Mutation	SNP	G	G	A	rs199536287		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AHNAK2	NM_138420	exon7	c.C5492T	p.P1831L	AACGACGGCATCT	.	342.0	17.0	84.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43243028	43243028	+	Missense_Mutation	SNP	G	G	C	rs138626640	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PSG3	NM_021016	exon2	c.C278G	p.P93R	TATGCAGGCCCAT	.	328.0	16.0	123.0	0.0	G|1.000;C|0.000	.	Atlas-SNP
PCDHGC5	56097	hgsc.bcm.edu	37	5	140869630	140869630	+	Missense_Mutation	SNP	G	G	A	rs2233603	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDHGC5	NM_018929	exon1	c.G823A	p.G275S	ACCAACGGCCAAC	.	173.0	7.0	64.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139276526	139276526	+	Splice_Site	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SNAPC4	NM_003086	exon18	c.2068-1G>A	.	CTCTTTCTGTAAG	.	48.0	14.0	30.0	0.0	.	.	Atlas-SNP
WBP4	11193	hgsc.bcm.edu	37	13	41656881	41656881	+	Missense_Mutation	SNP	A	A	G	rs115960433	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WBP4	NM_007187	exon10	c.A962G	p.Y321C	ATGAGTATGTATC	.	142.0	7.0	61.0	0.0	A|0.996;G|0.004	.	Atlas-SNP
ING5	84289	hgsc.bcm.edu	37	2	242648719	242648719	+	Silent	SNP	G	G	A	rs148010042	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_032329	exon3	c.G198A	p.Q66Q	CCTGCAGAAGATC	.	307.0	14.0	93.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
NHLRC2	374354	hgsc.bcm.edu	37	10	115664694	115664694	+	Missense_Mutation	SNP	C	C	T	rs150975627	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NHLRC2	NM_198514	exon10	c.C1823T	p.A608V	TGACTGCGTGTGC	.	102.0	7.0	54.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
B3GALT4	8705	hgsc.bcm.edu	37	6	33246031	33246031	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	B3GALT4	NM_003782	exon1	c.A835C	p.K279Q	ATTCTCAAGGTGG	.	42.0	14.0	14.0	0.0	.	.	Atlas-SNP
RALGPS2	55103	hgsc.bcm.edu	37	1	178846676	178846676	+	Silent	SNP	A	A	G	rs115273843	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RALGPS2	NM_152663	exon9	c.A651G	p.P217P	ATACCCATCAACT	.	277.0	16.0	120.0	0.0	A|0.997;G|0.003	.	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30703066	30703066	+	Silent	SNP	G	G	A	rs61736164	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TEX15	NM_031271	exon1	c.C3468T	p.S1156S	TGGATTGCTTACA	.	221.0	14.0	142.0	0.0	G|0.986;A|0.014	.	Atlas-SNP
ZCCHC6	79670	hgsc.bcm.edu	37	9	88938596	88938596	+	Missense_Mutation	SNP	C	C	T	rs188666254		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZCCHC6	NM_024617	exon13	c.G2069A	p.C690Y	ACCTTACAGGTAT	.	306.0	19.0	184.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
CCNI	10983	hgsc.bcm.edu	37	4	77969711	77969711	+	Silent	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCNI	NM_006835	exon7	c.C795G	p.L265L	GTGCTTGAGGGGA	.	158.0	62.0	77.0	0.0	.	.	Atlas-SNP
DPEP3	64180	hgsc.bcm.edu	37	16	68013593	68013593	+	Silent	SNP	G	G	A	rs56921747	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DPEP3	NM_001129758	exon2	c.C438T	p.S146S	ACCATGGCTGAAA	.	134.0	10.0	44.0	0.0	G|0.992;A|0.008	.	Atlas-SNP
ERBB2IP	55914	hgsc.bcm.edu	37	5	65349887	65349887	+	Missense_Mutation	SNP	A	A	G	rs34521887	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ERBB2IP	NM_001253699	exon21	c.A2741G	p.K914R	GGAGCAAGTCTGC	.	92.0	8.0	73.0	0.0	A|0.986;G|0.014	.	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143958	55143958	+	Missense_Mutation	SNP	C	C	G	rs61737863	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LILRB1	NM_001081637	exon6	c.C705G	p.I235M	TCCTATCGTGGCC	.	376.0	21.0	105.0	0.0	C|0.989;G|0.011	.	Atlas-SNP
PICALM	8301	hgsc.bcm.edu	37	11	85692193	85692193	+	Silent	SNP	G	G	A	rs12295435	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PICALM	NM_007166	exon17	c.C1758T	p.T586T	CCAAGCGGTTGTT	.	200.0	10.0	95.0	0.0	G|0.959;A|0.041	.	Atlas-SNP
SENP1	29843	hgsc.bcm.edu	37	12	48440205	48440205	+	Silent	SNP	G	G	A	rs34698661		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SENP1	NM_001267594	exon17	c.C1806T	p.D602D	CCCACAGTCACTT	.	253.0	20.0	114.0	0.0	G|0.993;A|0.007	.	Atlas-SNP
RAD54L2	23132	hgsc.bcm.edu	37	3	51677894	51677894	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RAD54L2	NM_015106	exon15	c.T2354G	p.L785R	TAGGGCTAGATGG	.	334.0	117.0	92.0	0.0	.	.	Atlas-SNP
ZNF462	58499	hgsc.bcm.edu	37	9	109687639	109687639	+	Silent	SNP	G	G	A	rs73522975	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF462	NM_021224	exon3	c.G1446A	p.S482S	GAGCTCGTTGAAA	.	164.0	9.0	49.0	0.0	G|0.990;A|0.010	.	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	37	16	57075912	57075912	+	Silent	SNP	G	G	A	rs73546859	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NLRC5	NM_032206	exon18	c.G3048A	p.L1016L	TGCTCTGGGGGAT	.	213.0	13.0	34.0	0.0	G|0.977;A|0.023	.	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3628493	3628493	+	Missense_Mutation	SNP	A	A	G	rs7223226	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GSG2	NM_031965	exon1	c.A1264G	p.N422D	TGTTCAAACCGGC	.	237.0	11.0	78.0	0.0	A|0.995;G|0.005	.	Atlas-SNP
VSIG10L	147645	hgsc.bcm.edu	37	19	51840536	51840536	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001163922	exon7	c.G2261T	p.G754V	TGGCCCCCCAGGA	.	70.0	22.0	26.0	0.0	.	.	Atlas-SNP
SLC2A5	6518	hgsc.bcm.edu	37	1	9098497	9098497	+	Silent	SNP	G	G	T	rs12564676	byfrequency;alternate_allele	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC2A5	NM_003039	exon10	c.C1167A	p.L389L	GGGCCCGAGGGCA	.	77.0	14.0	30.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76112290	76112290	+	Missense_Mutation	SNP	C	C	T	rs149983793	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DTX2	NM_001102596	exon2	c.C734T	p.A245V	CCTTTGCACCGTA	.	328.0	16.0	132.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79166166	79166166	+	Missense_Mutation	SNP	C	C	A	rs201824599		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AZI1	NM_014984	exon21	c.G2574T	p.Q858H	CTCCAGCTGCTGC	.	129.0	10.0	50.0	0.0	.	.	Atlas-SNP
CDK5RAP3	80279	hgsc.bcm.edu	37	17	46053278	46053278	+	Missense_Mutation	SNP	C	C	T	rs199625816		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CDK5RAP3	NM_176096	exon8	c.C697T	p.R233W	CAGAAGCGGGGAA	.	92.0	7.0	32.0	0.0	.	.	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140574266	140574266	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDHB10	NM_018930	exon1	c.G2141T	p.R714L	CGGTGCGGCTGTG	.	51.0	19.0	24.0	0.0	.	.	Atlas-SNP
KIDINS220	57498	hgsc.bcm.edu	37	2	8872078	8872078	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIDINS220	NM_020738	exon30	c.T4088G	p.L1363R	GAATTGAGACTCG	.	119.0	44.0	59.0	0.0	.	.	Atlas-SNP
PCDHGA7	56108	hgsc.bcm.edu	37	5	140764269	140764269	+	Silent	SNP	C	C	T	rs115492697	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_032087	exon1	c.C1803T	p.N601N	CCAGAACGCCTGG	.	161.0	10.0	60.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
TRIM34	53840	hgsc.bcm.edu	37	11	5662437	5662437	+	Missense_Mutation	SNP	G	G	C	rs74051049	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRIM34	NM_130390	exon4	c.G791C	p.R264T	TGGCCAGGAGTGG	.	381.0	18.0	194.0	0.0	G|0.970;C|0.030	.	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	37	10	101421367	101421367	+	Missense_Mutation	SNP	G	G	A	rs61729539	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ENTPD7	NM_020354	exon3	c.G173A	p.R58Q	TACCACGAGATAG	.	183.0	12.0	61.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
FBXO16	157574	hgsc.bcm.edu	37	8	28321156	28321156	+	Silent	SNP	G	G	A	rs149976851	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBXO16	NM_172366	exon4	c.C315T	p.D105D	CCGAGGGTCCAGG	.	131.0	8.0	73.0	0.0	G|1.000;A|0.000	.	Atlas-SNP
LEFTY1	10637	hgsc.bcm.edu	37	1	226076617	226076617	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LEFTY1	NM_020997	exon1	c.G150A	p.E50E	GACCAGCTCCTCC	.	149.0	12.0	49.0	0.0	.	.	Atlas-SNP
OSTM1	28962	hgsc.bcm.edu	37	6	108370473	108370473	+	Silent	SNP	T	T	C	rs146289365		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OSTM1	NM_014028	exon5	c.A933G	p.K311K	TTTGCGTTTCTTT	.	162.0	8.0	68.0	0.0	T|1.000;C|0.000	.	Atlas-SNP
WDR41	55255	hgsc.bcm.edu	37	5	76732219	76732219	+	Missense_Mutation	SNP	C	C	A	rs150624821	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WDR41	NM_018268	exon12	c.G1094T	p.G365V	AAAAAACCTAGAA	.	146.0	11.0	64.0	0.0	C|0.997;A|0.003	.	Atlas-SNP
CYP26B1	56603	hgsc.bcm.edu	37	2	72374849	72374849	+	Missense_Mutation	SNP	C	C	T	rs149453254	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CYP26B1	NM_019885	exon1	c.G115A	p.A39T	GAGTGGCGGCCCA	.	64.0	6.0	42.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
SEZ6L2	26470	hgsc.bcm.edu	37	16	29906673	29906673	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SEZ6L2	NM_001243332	exon5	c.G760A	p.G254R	CTTGTCCTTCTCC	.	151.0	60.0	27.0	0.0	.	.	Atlas-SNP
OR13F1	138805	hgsc.bcm.edu	37	9	107266824	107266824	+	Missense_Mutation	SNP	T	T	C	rs7018553	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR13F1	NM_001004485	exon1	c.T281C	p.F94S	TTTCATTCTCAGG	.	177.0	10.0	95.0	0.0	T|0.992;C|0.008	.	Atlas-SNP
KDM8	79831	hgsc.bcm.edu	37	16	27221810	27221810	+	Silent	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001145348	exon2	c.C480G	p.V160V	GCGGGTCTGTGAC	.	59.0	15.0	17.0	0.0	.	.	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17211764	17211764	+	Missense_Mutation	SNP	G	G	C	rs12325439	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	XYLT1	NM_022166	exon11	c.C2296G	p.P766A	CCACCGGCTCATC	.	242.0	14.0	93.0	0.0	G|0.998;C|0.002	.	Atlas-SNP
BEND2	139105	hgsc.bcm.edu	37	X	18234834	18234834	+	Silent	SNP	G	G	A	rs148252097	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BEND2	NM_001184767	exon2	c.C45T	p.V15V	GTCGTCGACAGTT	.	163.0	11.0	71.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	70902610	70902610	+	Missense_Mutation	SNP	G	G	A	rs79417681		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HYDIN	NM_001270974	exon66	c.C11173T	p.R3725W	TGATCCGCATATT	.	168.0	11.0	72.0	0.0	.	.	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73717635	73717635	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ALMS1	NM_015120	exon10	c.C8546T	p.P2849L	GCAGACCAAGTTC	.	192.0	13.0	88.0	0.0	.	.	Atlas-SNP
KIT	3815	hgsc.bcm.edu	37	4	55569945	55569945	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIT	NM_000222	exon5	c.G812C	p.R271P	ATGAACGTCAGGC	.	317.0	124.0	132.0	0.0	.	.	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	37	4	123159290	123159290	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIAA1109	NM_015312	exon26	c.A3618T	p.S1206S	CAAATCAGTGGGA	.	240.0	76.0	120.0	0.0	.	.	Atlas-SNP
TRIM28	10155	hgsc.bcm.edu	37	19	59059082	59059082	+	Splice_Site	SNP	T	T	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRIM28	NM_005762	exon5	c.839+2T>A	.	AGCTCGTAAGTGT	.	171.0	8.0	35.0	0.0	.	.	Atlas-SNP
TMEM155	132332	hgsc.bcm.edu	37	4	122681517	122681517	+	Missense_Mutation	SNP	T	T	A	rs145109523	alternate_allele	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMEM155	NM_152399	exon6	c.A325T	p.I109L	AAGTTATTGGGCT	.	277.0	87.0	95.0	0.0	T|1.000;C|0.000	.	Atlas-SNP
PCDHB5	26167	hgsc.bcm.edu	37	5	140516336	140516336	+	Silent	SNP	C	C	T	rs61741623		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDHB5	NM_015669	exon1	c.C1320T	p.V440V	CCTGGTCTCCGAC	.	185.0	9.0	106.0	0.0	C|0.986;T|0.014	.	Atlas-SNP
C19orf59	199675	hgsc.bcm.edu	37	19	7742594	7742594	+	Missense_Mutation	SNP	T	T	G	rs146421608	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	C19orf59	NM_174918	exon2	c.T166G	p.S56A	GGTCATTCACGAC	.	224.0	9.0	81.0	0.0	T|0.999;G|0.001	.	Atlas-SNP
ZNF532	55205	hgsc.bcm.edu	37	18	56651544	56651544	+	Missense_Mutation	SNP	G	G	A	rs143994649	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF532	NM_018181	exon11	c.G3752A	p.S1251N	AACCCAGCCACGA	.	225.0	12.0	72.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
MUC13	56667	hgsc.bcm.edu	37	3	124632002	124632002	+	Silent	SNP	C	C	T	rs140633855	bycluster;byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MUC13	NM_033049	exon8	c.G1167A	p.A389A	CACGCACGCACAC	.	170.0	15.0	65.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	113002415	113002415	+	Silent	SNP	C	C	T	rs141324680	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BOC	NM_033254	exon16	c.C2589T	p.G863G	CCTGGGCTCCATC	.	416.0	19.0	109.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
SERPINB3	6317	hgsc.bcm.edu	37	18	61324552	61324552	+	Missense_Mutation	SNP	C	C	A	rs150385073	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SERPINB3	NM_006919	exon6	c.G564T	p.K188N	AAATTTCTTCTCC	.	993.0	43.0	319.0	0.0	C|0.997;A|0.003	.	Atlas-SNP
VDAC2	7417	hgsc.bcm.edu	37	10	76971363	76971363	+	Silent	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	VDAC2	NM_001184783	exon3	c.A22C	p.R8R	GAGCTCAGATTGC	.	152.0	51.0	85.0	0.0	.	.	Atlas-SNP
NOP56	10528	hgsc.bcm.edu	37	20	2638880	2638880	+	Silent	SNP	G	G	A	rs61752514		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NOP56	NM_006392	exon12	c.G1725A	p.A575A	AGAGGCGGTTGGC	.	92.0	6.0	59.0	0.0	A|0.005;G|0.995	.	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91810850	91810850	+	Silent	SNP	G	G	C	rs140870303	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SV2B	NM_014848	exon9	c.G1185C	p.V395V	GGCCGTGGTTTGG	.	994.0	46.0	267.0	0.0	G|0.997;C|0.003	.	Atlas-SNP
ABCA10	10349	hgsc.bcm.edu	37	17	67152009	67152009	+	Silent	SNP	A	A	G	rs151287590	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ABCA10	NM_080282	exon30	c.T3513C	p.D1171D	ATCTTCATCTTCT	.	374.0	16.0	100.0	0.0	A|0.999;G|0.001	.	Atlas-SNP
OR2S2	56656	hgsc.bcm.edu	37	9	35958008	35958008	+	Missense_Mutation	SNP	C	C	T	rs2233559	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR2S2	NM_019897	exon1	c.G88A	p.V30M	TGAGCACGAAGAA	.	127.0	6.0	53.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
FANCC	2176	hgsc.bcm.edu	37	9	97934367	97934367	+	Silent	SNP	T	T	C	rs1800360	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FANCC	NM_001243743	exon5	c.A408G	p.Q136Q	AAGACCTTGAGTG	.	217.0	13.0	108.0	0.0	T|0.973;C|0.027	.	Atlas-SNP
PRR14L	253143	hgsc.bcm.edu	37	22	32113080	32113080	+	Silent	SNP	A	A	G	rs4296524	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRR14L	NM_173566	exon4	c.T745C	p.L249L	TAACTAATGTGCT	.	654.0	31.0	216.0	0.0	A|0.963;G|0.037	.	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151884447	151884447	+	Silent	SNP	C	C	T	rs61730536	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MLL3	NM_170606	exon33	c.G4908A	p.T1636T	CTTAAGCGTGCTT	.	158.0	9.0	54.0	0.0	C|0.962;T|0.038	.	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43653851	43653851	+	Missense_Mutation	SNP	A	A	C	rs142885180	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZSCAN29	NM_152455	exon5	c.T1979G	p.F660C	GGACCAAAGCTTT	.	229.0	10.0	119.0	0.0	A|0.998;C|0.002	.	Atlas-SNP
ADCY8	114	hgsc.bcm.edu	37	8	131896992	131896992	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADCY8	NM_001115	exon8	c.A1927G	p.T643A	TTCTTGTTAGGGC	.	644.0	204.0	93.0	0.0	.	.	Atlas-SNP
LINS	55180	hgsc.bcm.edu	37	15	101109598	101109598	+	Missense_Mutation	SNP	C	C	T	rs74039425	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LINS	NM_001040616	exon7	c.G2119A	p.G707R	ATATTCCCACTTC	.	175.0	10.0	82.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
CEACAM7	1087	hgsc.bcm.edu	37	19	42181429	42181429	+	Missense_Mutation	SNP	C	C	T	rs35494482	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CEACAM7	NM_006890	exon4	c.G709A	p.E237K	CTGACTCATCTGC	.	174.0	9.0	51.0	0.0	C|0.984;T|0.016	.	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17353337	17353337	+	Missense_Mutation	SNP	G	G	A	rs74993523	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	XYLT1	NM_022166	exon3	c.C421T	p.R141W	TCGGCCGATGAGA	.	163.0	7.0	59.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
IGDCC3	9543	hgsc.bcm.edu	37	15	65621283	65621283	+	Silent	SNP	C	C	T	rs146205195	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IGDCC3	NM_004884	exon14	c.G2409A	p.A803A	CCGGGCCGCTGCA	.	66.0	7.0	24.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
EMD	2010	hgsc.bcm.edu	37	X	153609368	153609368	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EMD	NM_000117	exon6	c.C576T	p.S192S	TATGTCCTCCTCA	.	80.0	55.0	25.0	0.0	.	.	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215990450	215990450	+	Silent	SNP	G	G	A	rs73090721	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	USH2A	NM_206933	exon48	c.C9459T	p.C3153C	TTTAGCGCATGGA	.	334.0	18.0	93.0	0.0	G|0.994;A|0.006	.	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41283901	41283901	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KCNQ4	NM_004700	exon3	c.C471T	p.C157C	ATGCTGCTGCCGC	.	77.0	33.0	22.0	0.0	.	.	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29221031	29221031	+	Silent	SNP	C	C	A	rs184438116		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FAM179A	NM_199280	exon3	c.C51A	p.A17A	CGTGGCCGTGTAC	.	324.0	13.0	75.0	0.0	C|0.996;A|0.004	.	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25021208	25021208	+	Silent	SNP	G	G	A	rs57834615	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PARP4	NM_006437	exon26	c.C3231T	p.S1077S	AAACAAGGACGGC	.	244.0	10.0	93.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109613970	109613970	+	Silent	SNP	C	C	T	rs112439513	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MYO16	NM_001198950	exon18	c.C2121T	p.S707S	GAACTCCGCCTTC	.	145.0	8.0	77.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3674170	3674170	+	Silent	SNP	G	G	A	rs61734520	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SIGLEC1	NM_023068	exon13	c.C3432T	p.A1144A	GGAGGTGGCATCC	.	98.0	17.0	17.0	0.0	G|0.980;A|0.020	.	Atlas-SNP
NAF1	92345	hgsc.bcm.edu	37	4	164085437	164085437	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NAF1	NM_138386	exon2	c.G472A	p.D158N	AATCATCATCTCC	.	464.0	153.0	196.0	0.0	.	.	Atlas-SNP
CALCOCO1	57658	hgsc.bcm.edu	37	12	54109000	54109000	+	Missense_Mutation	SNP	T	T	C	rs34311341	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CALCOCO1	NM_020898	exon10	c.A1370G	p.E457G	TCCTTCTCCCGGG	.	223.0	15.0	64.0	0.0	T|0.997;C|0.003	.	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105410769	105410769	+	Silent	SNP	A	A	G	rs191005153	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AHNAK2	NM_138420	exon7	c.T11019C	p.S3673S	GGGGAGACTCACA	.	255.0	18.0	64.0	0.0	A|0.997;G|0.003	.	Atlas-SNP
KIAA0586	9786	hgsc.bcm.edu	37	14	58923453	58923453	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIAA0586	NM_001244189	exon12	c.A1446C	p.K482N	AACTAAAGTGACT	.	314.0	105.0	99.0	0.0	.	.	Atlas-SNP
BMPER	168667	hgsc.bcm.edu	37	7	34118476	34118476	+	Silent	SNP	C	C	T	rs116085783	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BMPER	NM_133468	exon13	c.C1086T	p.G362G	GCCCGGCGTTTGC	.	133.0	6.0	46.0	0.0	C|0.991;T|0.009	.	Atlas-SNP
FAM218A	152756	hgsc.bcm.edu	37	4	165878567	165878567	+	Missense_Mutation	SNP	G	G	C	rs73871552	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_153027	exon1	c.G393C	p.R131S	CATCAGGTCCCAG	.	331.0	19.0	165.0	0.0	G|0.979;C|0.021	.	Atlas-SNP
APOA4	337	hgsc.bcm.edu	37	11	116693459	116693459	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	APOA4	NM_000482	exon2	c.T92C	p.M31T	TCCCACATCACCG	.	115.0	36.0	40.0	0.0	.	.	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8770875	8770875	+	Silent	SNP	A	A	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLCB1	NM_015192	exon31	c.C3390C	p.H1130H	CAAGGAAATACGT	.	304.0	18.0	135.0	0.0	.	.	Atlas-SNP
UFSP2	55325	hgsc.bcm.edu	37	4	186339770	186339770	+	Silent	SNP	A	A	G	rs78119878	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UFSP2	NM_018359	exon3	c.T237C	p.S79S	ACAAGCAGAAGCA	.	218.0	16.0	91.0	0.0	A|0.995;G|0.005	.	Atlas-SNP
MAP6	4135	hgsc.bcm.edu	37	11	75298206	75298206	+	Silent	SNP	C	C	T	rs151285396	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MAP6	NM_033063	exon4	c.G2340A	p.K780K	TTGAGTCTTCAGA	.	188.0	10.0	81.0	0.0	C|0.990;T|0.010	.	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108233547	108233547	+	Missense_Mutation	SNP	A	A	G	rs33940843	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FER	NM_005246	exon10	c.A1234G	p.M412V	ACATCTATGGTAA	.	258.0	12.0	139.0	0.0	A|0.977;G|0.023	.	Atlas-SNP
SUCLG2	8801	hgsc.bcm.edu	37	3	67546244	67546244	+	Missense_Mutation	SNP	T	T	C	rs9843840	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SUCLG2	NM_001177599	exon9	c.A1040G	p.K347R	AGCAATTTGAATG	.	162.0	7.0	59.0	0.0	T|0.980;C|0.020	.	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98110038	98110038	+	Missense_Mutation	SNP	T	T	C	rs73854830	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5K3	NM_001005516	exon1	c.T529C	p.F177L	AATCATTTTTTCT	.	336.0	15.0	103.0	0.0	T|0.946;C|0.054	.	Atlas-SNP
RNF148	378925	hgsc.bcm.edu	37	7	122342001	122342001	+	Silent	SNP	T	T	C	rs149475218		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RNF148	NM_198085	exon1	c.A804G	p.Q268Q	TACATCTTGGGGT	.	313.0	19.0	139.0	0.0	T|0.994;C|0.006	.	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39775245	39775245	+	Silent	SNP	C	C	T	rs74718295	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MACF1	NM_012090	exon25	c.C2808T	p.V936V	TAGGGTCGAACAA	.	189.0	9.0	84.0	0.0	C|0.988;T|0.012	.	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51769404	51769404	+	Missense_Mutation	SNP	C	C	T	rs187547602	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AGAP6	NM_001077665	exon8	c.C1519T	p.R507C	ATCCACCGCAGTC	.	268.0	14.0	68.0	0.0	C|0.994;T|0.006	.	Atlas-SNP
ZFHX3	463	hgsc.bcm.edu	37	16	72993238	72993238	+	Silent	SNP	G	G	A	rs150043800	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZFHX3	NM_006885	exon2	c.C807T	p.F269F	GCCATCGAATTTG	.	105.0	6.0	63.0	0.0	G|0.998;A|0.002	.	Atlas-SNP
CSTA	1475	hgsc.bcm.edu	37	3	122060390	122060390	+	Missense_Mutation	SNP	G	G	T	rs34021626	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CSTA	NM_005213	exon3	c.G273T	p.K91N	AAACAAGGATGAC	.	94.0	8.0	52.0	0.0	G|0.984;T|0.016	.	Atlas-SNP
DLL3	10683	hgsc.bcm.edu	37	19	39994732	39994732	+	Missense_Mutation	SNP	G	G	A	rs35380611	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DLL3	NM_016941	exon5	c.G674A	p.S225N	GCTGCAGCCCTGA	.	260.0	13.0	52.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684675	100684675	+	Silent	SNP	C	C	T	rs73402901	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MUC17	NM_001040105	exon3	c.C9978T	p.D3326D	TGCTGACGGTACT	.	181.0	8.0	49.0	0.0	C|0.988;T|0.012	.	Atlas-SNP
ITGAD	3681	hgsc.bcm.edu	37	16	31422071	31422071	+	Missense_Mutation	SNP	C	C	G	rs142278416	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ITGAD	NM_005353	exon12	c.C1228G	p.L410V	ACCGAGCTAGCCC	.	170.0	10.0	53.0	0.0	C|0.991;G|0.009	.	Atlas-SNP
EDIL3	10085	hgsc.bcm.edu	37	5	83356219	83356219	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EDIL3	NM_005711	exon9	c.T1037C	p.M346T	ATGTCCATGTTGA	.	344.0	114.0	130.0	0.0	.	.	Atlas-SNP
TRMT2A	27037	hgsc.bcm.edu	37	22	20100181	20100181	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRMT2A	NM_022727	exon12	c.A1783T	p.T595S	CCCCTGTGCCATT	.	539.0	22.0	150.0	0.0	.	.	Atlas-SNP
COPB2	9276	hgsc.bcm.edu	37	3	139077081	139077081	+	Silent	SNP	C	C	T	rs141832843	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COPB2	NM_004766	exon21	c.G2586A	p.P862P	AATAACCGGAGTA	.	498.0	30.0	310.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186815	12186815	+	Missense_Mutation	SNP	C	C	T	rs193079644	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001136501	exon4	c.C880T	p.H294Y	TGGTTCCATTCCT	.	152.0	11.0	60.0	0.0	C|0.999;T|0.000	.	Atlas-SNP
SETBP1	26040	hgsc.bcm.edu	37	18	42530796	42530796	+	Silent	SNP	G	G	A	rs113053616	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SETBP1	NM_015559	exon4	c.G1491A	p.P497P	TAAGCCGCGGAAG	.	140.0	10.0	47.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	95891985	95891985	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLCE1	NM_016341	exon3	c.C1261T	p.H421Y	CTACTCCATTTCC	.	123.0	18.0	54.0	0.0	.	.	Atlas-SNP
OR4D9	390199	hgsc.bcm.edu	37	11	59282608	59282608	+	Missense_Mutation	SNP	T	T	G	rs116643910	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR4D9	NM_001004711	exon1	c.T223G	p.S75A	TTTTCCTCCATCA	.	314.0	15.0	117.0	0.0	T|0.986;G|0.014	.	Atlas-SNP
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606280	1606280	+	Missense_Mutation	SNP	C	C	G	rs139668171	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KRTAP5-1	NM_001005922	exon1	c.G200C	p.G67A	CAGCCCCCTTTGC	.	264.0	11.0	102.0	0.0	C|0.994;G|0.006	.	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62291087	62291087	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AHNAK	NM_001620	exon5	c.A10802G	p.K3601R	GGCATCTTCAGAT	.	220.0	9.0	75.0	0.0	.	.	Atlas-SNP
OR2M3	127062	hgsc.bcm.edu	37	1	248367162	248367162	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR2M3	NM_001004689	exon1	c.G793T	p.D265Y	ACATCTGATCGCT	.	367.0	114.0	121.0	0.0	.	.	Atlas-SNP
TMF1	7110	hgsc.bcm.edu	37	3	69079037	69079037	+	Silent	SNP	T	T	C	rs61737464		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TMF1	NM_007114	exon11	c.A2523G	p.E841E	ACTGTTTTCCTGT	.	325.0	13.0	101.0	0.0	T|0.994;C|0.006	.	Atlas-SNP
ZNF808	388558	hgsc.bcm.edu	37	19	53056571	53056571	+	Missense_Mutation	SNP	G	G	C	rs329964	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001039886	exon5	c.G402C	p.K134N	AAAAAAGTTGACT	.	592.0	24.0	162.0	0.0	G|0.983;C|0.017	.	Atlas-SNP
TRABD	80305	hgsc.bcm.edu	37	22	50636268	50636268	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRABD	NM_025204	exon8	c.C688A	p.R230S	GTGGAACGCTGCA	.	59.0	24.0	19.0	0.0	.	.	Atlas-SNP
OR10A5	144124	hgsc.bcm.edu	37	11	6867015	6867015	+	Silent	SNP	T	T	C	rs7952340	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR10A5	NM_178168	exon1	c.T102C	p.T34T	TCTAACTATCTAT	.	352.0	21.0	150.0	0.0	T|0.983;C|0.017	.	Atlas-SNP
CCT8L2	150160	hgsc.bcm.edu	37	22	17072347	17072347	+	Nonsense_Mutation	SNP	C	C	T	rs139948519	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCT8L2	NM_014406	exon1	c.G1094A	p.W365X	CATTCCCATTCAA	.	72.0	5.0	48.0	0.0	C|0.982;T|0.018	.	Atlas-SNP
PSMD3	5709	hgsc.bcm.edu	37	17	38140666	38140666	+	Missense_Mutation	SNP	T	T	C	rs78909252	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PSMD3	NM_002809	exon2	c.T340C	p.Y114H	GTTCTGTATAAGG	.	197.0	9.0	78.0	0.0	T|0.989;C|0.011	.	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6303322	6303322	+	Silent	SNP	C	C	T	rs71524362	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WFS1	NM_001145853	exon8	c.C1800T	p.T600T	AGTCACCGTGGCG	.	222.0	10.0	56.0	0.0	C|0.987;T|0.013	.	Atlas-SNP
TCEANC	170082	hgsc.bcm.edu	37	X	13681057	13681057	+	Silent	SNP	T	T	C	rs7061978	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TCEANC	NM_152634	exon4	c.T520C	p.L174L	ATTCAATTGAAAC	.	118.0	8.0	45.0	0.0	T|0.962;C|0.038	.	Atlas-SNP
OR1K1	392392	hgsc.bcm.edu	37	9	125562623	125562623	+	Silent	SNP	C	C	T	rs140842320	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR1K1	NM_080859	exon1	c.C222T	p.F74F	CTGCTTCGCCTCC	.	198.0	11.0	68.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
ATP6V0D2	245972	hgsc.bcm.edu	37	8	87155151	87155151	+	Missense_Mutation	SNP	G	G	A	rs149665160	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATP6V0D2	NM_152565	exon5	c.G607A	p.V203I	GGTGATGTCACAG	.	264.0	11.0	45.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
DMAP1	55929	hgsc.bcm.edu	37	1	44684035	44684035	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DMAP1	NM_001034023	exon5	c.A446G	p.D149G	TCCACGATGATGC	.	279.0	99.0	94.0	0.0	.	.	Atlas-SNP
WHSC1L1	54904	hgsc.bcm.edu	37	8	38153339	38153339	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WHSC1L1	NM_023034	exon16	c.G2890A	p.V964I	CCCAAACAATCTG	.	116.0	10.0	64.0	0.0	.	.	Atlas-SNP
FBP2	8789	hgsc.bcm.edu	37	9	97333825	97333825	+	Silent	SNP	G	G	A	rs73531436	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBP2	NM_003837	exon4	c.C486T	p.A162A	ACCTGCGGCCACA	.	84.0	7.0	36.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
FBXW8	26259	hgsc.bcm.edu	37	12	117423069	117423069	+	Silent	SNP	C	C	T	rs138454816	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBXW8	NM_153348	exon6	c.C894T	p.H298H	TGAGCACGATGCA	.	239.0	12.0	120.0	0.0	C|0.989;T|0.011	.	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	37	5	141028552	141028552	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FCHSD1	NM_033449	exon7	c.G548A	p.R183Q	CTGGTCCGAGAGT	.	397.0	20.0	105.0	0.0	.	.	Atlas-SNP
PRMT5	10419	hgsc.bcm.edu	37	14	23396003	23396003	+	Missense_Mutation	SNP	C	C	G	rs113488776	alternate_allele	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRMT5	NM_006109	exon5	c.G471C	p.L157F	TGCCACCAAGGGT	.	355.0	15.0	111.0	0.0	C|0.500;T|0.500	.	Atlas-SNP
APC	324	hgsc.bcm.edu	37	5	112175242	112175242	+	Silent	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	APC,bladder,carcinoma,+2	APC	NM_001127510	exon17	c.A3951G	p.E1317E	AGCTGAAGATCCT	.	225.0	13.0	107.0	1.0	.	.	Atlas-SNP
GRM1	2911	hgsc.bcm.edu	37	6	146755304	146755304	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GRM1	NM_000838	exon9	c.C2957A	p.A986E	GCGCGGCGACCAC	.	96.0	29.0	38.0	0.0	.	.	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41573197	41573197	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ANK1	NM_001142446	exon14	c.G1674T	p.K558N	TGCTTCCTTTTCC	.	53.0	27.0	28.0	0.0	.	.	Atlas-SNP
COA4	51287	hgsc.bcm.edu	37	11	73584353	73584353	+	Missense_Mutation	SNP	G	G	A	rs35017327	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_016565	exon2	c.C71T	p.P24L	TCCAGCGGGTCCT	.	126.0	7.0	52.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151879584	151879584	+	Silent	SNP	T	T	C	rs61730538	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MLL3	NM_170606	exon36	c.A5361G	p.Q1787Q	ACCAAATTGCTGT	.	460.0	20.0	133.0	0.0	T|0.964;C|0.036	.	Atlas-SNP
GBP6	163351	hgsc.bcm.edu	37	1	89849256	89849256	+	Missense_Mutation	SNP	G	G	A	rs116173091	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GBP6	NM_198460	exon9	c.G1411A	p.E471K	GTGATAGAGGAAT	.	421.0	24.0	132.0	0.0	G|0.986;A|0.014	.	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6335130	6335130	+	Missense_Mutation	SNP	G	G	A	rs138218829		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MCPH1	NM_024596	exon10	c.G1951A	p.V651I	ACATTAGTCATGA	.	194.0	10.0	76.0	0.0	G|0.999;A|0.000	.	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30916843	30916843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DPCR1	NM_080870	exon2	c.C602A	p.T201N	CAAGTACCAGCTC	.	188.0	65.0	97.0	0.0	.	.	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156946940	156946940	+	Silent	SNP	C	C	T	rs34711517	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADAM19	NM_033274	exon6	c.G507A	p.P169P	CGGGGGCGGCTTG	.	199.0	11.0	67.0	0.0	C|0.984;T|0.016	.	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	32456459	32456459	+	Missense_Mutation	SNP	G	G	A	rs143184877	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DMD	NM_004006	exon29	c.C3970T	p.R1324C	ATATGCGAATCTG	.	245.0	19.0	97.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
ITGA9	3680	hgsc.bcm.edu	37	3	37670679	37670679	+	Missense_Mutation	SNP	G	G	A	rs61751189	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ITGA9	NM_002207	exon16	c.G1691A	p.R564Q	TTCAGCGGAGGGT	.	176.0	10.0	83.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
OR2J2	26707	hgsc.bcm.edu	37	6	29141732	29141732	+	Missense_Mutation	SNP	C	C	A	rs114093208	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR2J2	NM_030905	exon1	c.C320A	p.A107E	TTCTTGCACTGGG	.	596.0	35.0	197.0	0.0	C|0.995;A|0.005	.	Atlas-SNP
OXER1	165140	hgsc.bcm.edu	37	2	42991312	42991312	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OXER1	NM_148962	exon1	c.G8T	p.C3F	CGGTGACACAACA	.	135.0	39.0	45.0	0.0	.	.	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175306758	175306758	+	Missense_Mutation	SNP	G	G	A	rs61731114	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TNR	NM_003285	exon19	c.C3440T	p.T1147I	CTCAAAGTGTCTC	.	82.0	5.0	37.0	0.0	G|0.989;A|0.011	.	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35861023	35861023	+	Missense_Mutation	SNP	C	C	T	rs138482569		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IL7R	NM_002185	exon2	c.C152T	p.S51L	ATGGATCGCAGCA	.	246.0	11.0	107.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541497	12541497	+	Missense_Mutation	SNP	T	T	C	rs115487665	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF443	NM_005815	exon4	c.A1489G	p.T497A	TGTGAGTTGTTTT	.	171.0	8.0	89.0	0.0	T|0.994;C|0.006	.	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101816873	101816873	+	Missense_Mutation	SNP	A	A	G	rs35642150	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COL15A1	NM_001855	exon32	c.A2966G	p.K989R	GAGAGAAAGGATC	.	184.0	12.0	96.0	0.0	A|0.988;G|0.012	.	Atlas-SNP
ZNF644	84146	hgsc.bcm.edu	37	1	91406186	91406186	+	Missense_Mutation	SNP	G	G	A	rs143932357	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF644	NM_201269	exon3	c.C725T	p.T242M	ATTCCCGTTACTG	.	162.0	10.0	91.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
ECT2L	345930	hgsc.bcm.edu	37	6	139170526	139170526	+	Missense_Mutation	SNP	G	G	A	rs76241582	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ECT2L	NM_001195037	exon8	c.G1024A	p.G342R	AGCATCGGAATAT	.	187.0	10.0	78.0	0.0	G|0.989;A|0.011	.	Atlas-SNP
PPAP2C	8612	hgsc.bcm.edu	37	19	282149	282149	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PPAP2C	NM_177543	exon5	c.G765A	p.L255L	AGCCACCAGTGCC	.	29.0	11.0	19.0	0.0	.	.	Atlas-SNP
CDHR4	389118	hgsc.bcm.edu	37	3	49830624	49830624	+	Missense_Mutation	SNP	G	G	T	rs143779889	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001007540	exon13	c.C1744A	p.R582S	TCAGGCGCTGTGG	.	117.0	9.0	37.0	0.0	G|0.999;T|0.001	.	Atlas-SNP
CHMP7	91782	hgsc.bcm.edu	37	8	23115893	23115893	+	Silent	SNP	C	C	T	rs115402987	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CHMP7	NM_152272	exon7	c.C891T	p.A297A	CGAGGCCTTGCAT	.	81.0	6.0	39.0	0.0	C|0.990;T|0.010	.	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8662139	8662139	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRIM66	NM_014818	exon9	c.C1348G	p.Q450E	GCTGCTGAAAGTG	.	94.0	34.0	57.0	0.0	.	.	Atlas-SNP
GBP2	2634	hgsc.bcm.edu	37	1	89575396	89575396	+	Missense_Mutation	SNP	C	C	T	rs146553595		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GBP2	NM_004120	exon10	c.G1623A	p.M541I	CTCTGCCATTAAC	.	370.0	19.0	125.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
ANKRD53	79998	hgsc.bcm.edu	37	2	71206977	71206977	+	Missense_Mutation	SNP	G	G	A	rs149813455	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ANKRD53	NM_001115116	exon3	c.G604A	p.A202T	AAAGGCGCAGACC	.	124.0	7.0	51.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
RIMKLA	284716	hgsc.bcm.edu	37	1	42880228	42880228	+	Silent	SNP	C	C	T	rs113242727	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RIMKLA	NM_173642	exon5	c.C759T	p.G253G	CCTAGGCATGGAC	.	196.0	11.0	119.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55441956	55441956	+	Silent	SNP	G	G	A	rs61750468	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NLRP7	NM_001127255	exon9	c.C2721T	p.N907N	GTCCAGGTTTGTG	.	232.0	10.0	63.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6303319	6303319	+	Silent	SNP	C	C	A	rs71524361	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	WFS1	NM_001145853	exon8	c.C1797A	p.V599V	CGCAGTCACCGTG	.	220.0	11.0	58.0	0.0	A|0.013;C|0.987	.	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	168812942	168812942	+	Missense_Mutation	SNP	G	G	A	rs34224062	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MECOM	NM_004991	exon13	c.C2941T	p.H981Y	ATAAGTGACACTT	.	388.0	17.0	126.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
AMOT	154796	hgsc.bcm.edu	37	X	112053138	112053138	+	Silent	SNP	C	C	T	rs57201849	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AMOT	NM_001113490	exon4	c.G1614A	p.S538S	GAGCTGCGAGATG	.	136.0	15.0	41.0	0.0	C|0.980;T|0.020	.	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72948639	72948639	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRPA1	NM_007332	exon21	c.G2439T	p.T813T	GCCCGTCGTGTAG	.	560.0	76.0	117.0	0.0	.	.	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33550538	33550538	+	Silent	SNP	A	A	G	rs114003632	byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001244752	exon10	c.A1989G	p.T663T	TGAGACATGGACT	.	342.0	15.0	154.0	0.0	A|0.982;G|0.018	.	Atlas-SNP
PLEKHG5	57449	hgsc.bcm.edu	37	1	6528320	6528320	+	Missense_Mutation	SNP	C	C	T	rs61737997	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLEKHG5	NM_001265592	exon21	c.G2813A	p.R938H	CGGCGGCGGAGAC	.	193.0	13.0	60.0	0.0	C|0.973;T|0.027	.	Atlas-SNP
CCIN	881	hgsc.bcm.edu	37	9	36170397	36170397	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCIN	NM_005893	exon1	c.T898C	p.Y300H	TTTGCTTATATCA	.	60.0	18.0	20.0	0.0	.	.	Atlas-SNP
PEX5L	51555	hgsc.bcm.edu	37	3	179537713	179537713	+	Silent	SNP	G	G	T	rs28682295	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PEX5L	NM_016559	exon9	c.C874A	p.R292R	TCCTCCGAGCCAT	.	439.0	22.0	170.0	0.0	G|0.993;T|0.007	.	Atlas-SNP
HTR3C	170572	hgsc.bcm.edu	37	3	183778004	183778004	+	Missense_Mutation	SNP	G	G	T	rs76183574	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HTR3C	NM_130770	exon9	c.G1208T	p.G403V	ATGGGGGCTCAGG	.	158.0	8.0	50.0	0.0	G|0.995;T|0.005	.	Atlas-SNP
ZNF669	79862	hgsc.bcm.edu	37	1	247265410	247265410	+	Silent	SNP	C	C	T	rs61730465	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF669	NM_024804	exon2	c.G267A	p.S89S	AGCCACCGAGTCC	.	266.0	12.0	96.0	0.0	C|0.992;T|0.008	.	Atlas-SNP
XPNPEP2	7512	hgsc.bcm.edu	37	X	128881685	128881685	+	Missense_Mutation	SNP	C	C	T	rs191887278	by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	XPNPEP2	NM_003399	exon7	c.C593T	p.P198L	GGCCACCGGTTCC	.	79.0	9.0	42.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
ZNF385C	201181	hgsc.bcm.edu	37	17	40183707	40183707	+	Silent	SNP	G	G	C	rs75049227		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF385C	NM_001242704	exon4	c.C369G	p.A123A	ATCCTGGGCCTGG	.	600.0	24.0	149.0	0.0	G|0.994;C|0.006	.	Atlas-SNP
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37732721	37732721	+	Missense_Mutation	SNP	G	G	A	rs113560526	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RAB11FIP1	NM_025151	exon3	c.C934T	p.L312F	GGGAAAGGACATC	.	112.0	8.0	57.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
CD5	921	hgsc.bcm.edu	37	11	60889246	60889246	+	Silent	SNP	C	C	T	rs34821010	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CD5	NM_014207	exon6	c.C969T	p.S323S	TGGCAGCGTCAAC	.	158.0	17.0	50.0	0.0	C|0.989;T|0.011	.	Atlas-SNP
MPDU1	9526	hgsc.bcm.edu	37	17	7490798	7490798	+	Missense_Mutation	SNP	G	G	A	rs16956808	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MPDU1	NM_004870	exon7	c.G673A	p.G225S	TGCAACGGCCTCA	.	101.0	8.0	39.0	0.0	G|0.960;A|0.040	.	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151877889	151877889	+	Silent	SNP	G	G	C	rs17173370	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MLL3	NM_170606	exon36	c.C7056G	p.V2352V	TTGGGAGACACCA	.	283.0	12.0	133.0	0.0	G|0.954;C|0.046	.	Atlas-SNP
HLCS	3141	hgsc.bcm.edu	37	21	38302554	38302554	+	Silent	SNP	C	C	T	rs111603166	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HLCS	NM_000411	exon6	c.G1176A	p.A392A	CACCTCCGCAGCT	.	132.0	12.0	38.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
ANGPTL1	9068	hgsc.bcm.edu	37	1	178834201	178834201	+	Silent	SNP	G	G	A	rs77089478	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ANGPTL1	NM_004673	exon3	c.C711T	p.N237N	AATCTCGTTACCT	.	111.0	10.0	38.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
RFT1	91869	hgsc.bcm.edu	37	3	53156464	53156464	+	Missense_Mutation	SNP	G	G	A	rs140127085	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RFT1	NM_052859	exon4	c.C382T	p.L128F	CCGAGAGACCAAA	.	390.0	17.0	149.0	0.0	G|0.997;A|0.003	.	Atlas-SNP
KCNK7	10089	hgsc.bcm.edu	37	11	65363063	65363063	+	Missense_Mutation	SNP	C	C	T	rs78680181	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KCNK7	NM_005714	exon1	c.G181A	p.G61R	GAGCTCCGGGTGG	.	61.0	5.0	19.0	0.0	C|0.981;T|0.019	.	Atlas-SNP
CEP120	153241	hgsc.bcm.edu	37	5	122718561	122718561	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CEP120	NM_153223	exon14	c.A1883C	p.K628T	GACGGCTTTTGCT	.	232.0	70.0	131.0	0.0	.	.	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23909670	23909670	+	Missense_Mutation	SNP	G	G	A	rs61742500	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SACS	NM_014363	exon10	c.C8345T	p.A2782V	ACAGATGCATGAA	.	176.0	11.0	47.0	0.0	G|0.994;A|0.006	.	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17779907	17779907	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KIF13A	NM_001105566	exon32	c.G3855A	p.T1285T	ACTCTGCGTGAAA	.	194.0	9.0	93.0	0.0	.	.	Atlas-SNP
DENND4C	55667	hgsc.bcm.edu	37	9	19332034	19332034	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DENND4C	NM_017925	exon17	c.C2312T	p.A771V	AGTGGGCCAAGTG	.	484.0	88.0	198.0	0.0	.	.	Atlas-SNP
CARD17	440068	hgsc.bcm.edu	37	11	104971273	104971273	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CARD17	NM_001007232	exon2	c.A241G	p.S81G	GGTGACTGTCTTC	.	254.0	92.0	96.0	0.0	.	.	Atlas-SNP
SLC35D2	11046	hgsc.bcm.edu	37	9	99099049	99099049	+	Silent	SNP	T	T	C	rs35044811	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC35D2	NM_007001	exon9	c.A702G	p.Q234Q	CTTCCATTGGTTG	.	181.0	12.0	97.0	0.0	T|0.997;C|0.003	.	Atlas-SNP
HOGA1	112817	hgsc.bcm.edu	37	10	99361690	99361690	+	Silent	SNP	G	G	A	rs34820265	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HOGA1	NM_138413	exon6	c.G777A	p.T259T	CTGCACGGGGCAA	.	146.0	8.0	17.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
LAT2	7462	hgsc.bcm.edu	37	7	73638471	73638471	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LAT2	NM_032464	exon12	c.A572G	p.E191G	AATCTGAGGATTA	.	103.0	42.0	24.0	0.0	.	.	Atlas-SNP
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209933659	209933659	+	Missense_Mutation	SNP	G	G	A	rs78296889	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TRAF3IP3	NM_025228	exon3	c.G275A	p.R92Q	CCAGGCGGCCAGG	.	174.0	11.0	65.0	0.0	G|0.984;A|0.016	.	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81232391	81232391	+	Silent	SNP	T	T	A	rs116372721		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PKD1L2	NM_001076780	exon7	c.A1419T	p.S473S	AGCCAATGAGATG	.	202.0	11.0	114.0	0.0	T|0.998;A|0.002	.	Atlas-SNP
BTBD3	22903	hgsc.bcm.edu	37	20	11900425	11900425	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BTBD3	NM_014962	exon3	c.G477A	p.E159E	TGCAGAGGACAAA	.	268.0	16.0	81.0	0.0	.	.	Atlas-SNP
AMDHD1	144193	hgsc.bcm.edu	37	12	96354236	96354236	+	Missense_Mutation	SNP	G	G	T	rs143136011	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AMDHD1	NM_152435	exon5	c.G648T	p.K216N	GCTGAAGGAACTT	.	248.0	11.0	118.0	0.0	G|0.987;T|0.013	.	Atlas-SNP
UGT2B17	7367	hgsc.bcm.edu	37	4	69416569	69416569	+	Missense_Mutation	SNP	C	C	T	rs145097129	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UGT2B17	NM_001077	exon5	c.G1139A	p.G380D	TAGATGCCATTGG	.	43.0	19.0	2.0	0.0	C|0.995;T|0.005	.	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464934	10464934	+	Missense_Mutation	SNP	G	G	A	rs74968439		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RP1L1	NM_178857	exon4	c.C6674T	p.P2225L	CCTTCTGGCTCTG	.	113.0	10.0	62.0	0.0	G|0.987;A|0.013	.	Atlas-SNP
COPG1	22820	hgsc.bcm.edu	37	3	128994119	128994119	+	Silent	SNP	C	C	T	rs79019010	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_016128	exon23	c.C2478T	p.H826H	CACCCACACGTTG	.	156.0	21.0	45.0	0.0	C|0.991;T|0.009	.	Atlas-SNP
LEFTY2	7044	hgsc.bcm.edu	37	1	226125207	226125207	+	Silent	SNP	G	G	A	rs112610798	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LEFTY2	NM_003240	exon4	c.C1035T	p.N345N	CCTCATGTTGGGC	.	158.0	9.0	57.0	0.0	G|0.995;A|0.005	.	Atlas-SNP
RASSF9	9182	hgsc.bcm.edu	37	12	86199536	86199536	+	Silent	SNP	T	T	C	rs148047831		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RASSF9	NM_005447	exon2	c.A252G	p.R84R	GGAGCCTCTCCAC	.	270.0	12.0	85.0	0.0	T|0.994;C|0.006	.	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464890	10464890	+	Missense_Mutation	SNP	C	C	G	rs80000074		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RP1L1	NM_178857	exon4	c.G6718C	p.E2240Q	CTGACTCTGGCTG	.	95.0	7.0	56.0	0.0	C|0.987;G|0.013	.	Atlas-SNP
ATP2C1	27032	hgsc.bcm.edu	37	3	130688175	130688175	+	Missense_Mutation	SNP	G	G	A	rs41434650	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATP2C1	NM_001199181	exon16	c.G1450A	p.A484T	AGAAAAGCTGAAT	.	419.0	18.0	147.0	0.0	G|0.989;A|0.011	.	Atlas-SNP
FBXO38	81545	hgsc.bcm.edu	37	5	147818022	147818022	+	Silent	SNP	C	C	T	rs144172824	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FBXO38	NM_030793	exon18	c.C2760T	p.P920P	GCCACCCGAGAGA	.	129.0	12.0	77.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186344137	186344137	+	Silent	SNP	G	G	A	rs75545265	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TPR	NM_003292	exon1	c.C24T	p.V8V	CTCCAGGACTTGC	.	153.0	8.0	59.0	0.0	G|0.957;A|0.043	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113662543	113662543	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CSMD3	NM_198123	exon19	c.G3040T	p.G1014C	GTATGCCAGGGTC	.	462.0	154.0	63.0	0.0	.	.	Atlas-SNP
CAMSAP3	57662	hgsc.bcm.edu	37	19	7675999	7675999	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001080429	exon11	c.C1149G	p.F383L	CACCTTCCGCCAC	.	153.0	41.0	27.0	0.0	.	.	Atlas-SNP
RUNX1T1	862	hgsc.bcm.edu	37	8	93023262	93023262	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RUNX1T1	NM_001198679	exon5	c.C703A	p.P235T	TCAGTGGGAAGTT	.	367.0	131.0	82.0	0.0	.	.	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139904282	139904282	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ABCA2	NM_212533	exon43	c.G6659A	p.G2220D	TTGTTGCCGCCGC	.	129.0	38.0	70.0	0.0	.	.	Atlas-SNP
VSIG10L	147645	hgsc.bcm.edu	37	19	51840537	51840537	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001163922	exon7	c.G2260T	p.G754W	GGCCCCCCAGGAT	.	71.0	25.0	26.0	0.0	.	.	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983399	97983399	+	Missense_Mutation	SNP	T	T	C	rs113206717	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR5H6	NM_001005479	exon1	c.T271C	p.S91P	TTATCATCCACAG	.	950.0	55.0	317.0	0.0	T|0.978;C|0.022	.	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65300716	65300716	+	Missense_Mutation	SNP	C	C	A	rs75831552	byfrequency;by1000genomes	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	EYS	NM_001142800	exon26	c.G5044T	p.D1682Y	TCAAATCAGAATT	.	176.0	9.0	77.0	0.0	C|0.986;A|0.014	.	Atlas-SNP
OR51M1	390059	hgsc.bcm.edu	37	11	5411028	5411028	+	Missense_Mutation	SNP	C	C	T	rs74683499	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OR51M1	NM_001004756	exon1	c.C400T	p.R134C	TTTGACCGCCTTG	.	256.0	14.0	73.0	0.0	C|0.982;T|0.018	.	Atlas-SNP
DYM	54808	hgsc.bcm.edu	37	18	46905042	46905042	+	Missense_Mutation	SNP	C	C	T	rs150635814	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DYM	NM_017653	exon5	c.G316A	p.A106T	ACAAAGCATTGTG	.	193.0	8.0	82.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153222195	153222195	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HCFC1	NM_005334	exon15	c.C2516G	p.P839R	TGTCCCGGGGCCC	.	52.0	34.0	17.0	0.0	.	.	Atlas-SNP
ZNF607	84775	hgsc.bcm.edu	37	19	38190665	38190665	+	Missense_Mutation	SNP	A	A	G	rs35735839	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF607	NM_032689	exon5	c.T367C	p.F123L	GACTAAAGGACTT	.	303.0	13.0	95.0	0.0	A|0.987;G|0.013	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113662542	113662542	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CSMD3	NM_198123	exon19	c.G3041A	p.G1014D	GGTATGCCAGGGT	.	463.0	155.0	63.0	0.0	.	.	Atlas-SNP
UBE2U	148581	hgsc.bcm.edu	37	1	64686577	64686577	+	Missense_Mutation	SNP	C	C	T	rs139887828	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	UBE2U	NM_152489	exon6	c.C493T	p.R165C	GACCCACGTAAAT	.	404.0	21.0	182.0	0.0	C|0.991;T|0.009	.	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46932145	46932145	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CELSR1	NM_014246	exon1	c.A923G	p.D308G	ACGCTGTCCGTGC	.	71.0	21.0	26.0	0.0	.	.	Atlas-SNP
PCDHA9	9752	hgsc.bcm.edu	37	5	140228494	140228494	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PCDHA9	NM_031857	exon1	c.G414T	p.K138N	ACAAAAGAATCTG	.	356.0	18.0	177.0	0.0	.	.	Atlas-SNP
C3orf79	152118	hgsc.bcm.edu	37	3	153220258	153220258	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001101337	exon3	c.C290A	p.A97D	CAGATGCCAGTCA	.	109.0	36.0	53.0	0.0	.	.	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41870245	41870245	+	Missense_Mutation	SNP	C	C	T	rs1042057	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TYRO3	NM_006293	exon19	c.C2444T	p.A815V	CCACTGCGGGAGG	.	121.0	8.0	49.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220421395	220421395	+	Missense_Mutation	SNP	C	C	T	rs140214067		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	OBSL1	NM_001173431	exon13	c.G4117A	p.E1373K	CGCCCTCGTGGAC	.	211.0	12.0	52.0	0.0	C|0.990;T|0.010	.	Atlas-SNP
GALNT13	114805	hgsc.bcm.edu	37	2	155158038	155158038	+	Silent	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GALNT13	NM_052917	exon9	c.C1092T	p.N364N	CAAGAACAACAGG	.	600.0	26.0	191.0	0.0	.	.	Atlas-SNP
APPL1	26060	hgsc.bcm.edu	37	3	57291288	57291288	+	Missense_Mutation	SNP	C	C	T	rs35776173	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	APPL1	NM_012096	exon15	c.C1262T	p.P421L	GGCCACCGACAGC	.	249.0	15.0	92.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
PLEKHN1	84069	hgsc.bcm.edu	37	1	907676	907676	+	Missense_Mutation	SNP	A	A	T	rs145042066	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PLEKHN1	NM_001160184	exon10	c.A910T	p.I304F	CCCCTCATCAACA	.	86.0	5.0	33.0	0.0	A|0.998;T|0.002	.	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133372234	133372234	+	Missense_Mutation	SNP	T	T	C	rs199655255		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TOPBP1	NM_007027	exon7	c.A877G	p.M293V	TGGGCATAGTCTT	.	574.0	30.0	159.0	0.0	.	.	Atlas-SNP
PRKDC	5591	hgsc.bcm.edu	37	8	48792051	48792051	+	Splice_Site	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRKDC	NM_001081640	exon40	c.5234+1G>T	.	AACTAACCTTTTT	.	217.0	69.0	53.0	0.0	.	.	Atlas-SNP
PRELP	5549	hgsc.bcm.edu	37	1	203455838	203455838	+	Silent	SNP	C	C	A	rs78674036	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PRELP	NM_201348	exon3	c.C978A	p.I326I	AGAAATCAACGGA	.	133.0	6.0	52.0	0.0	C|0.989;A|0.011	.	Atlas-SNP
SUCLA2	8803	hgsc.bcm.edu	37	13	48571139	48571139	+	Missense_Mutation	SNP	A	A	C	rs62636645	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SUCLA2	NM_003850	exon2	c.T110G	p.L37W	TTAAACAATCCAG	.	367.0	17.0	71.0	0.0	A|0.971;C|0.029	.	Atlas-SNP
NOP14	8602	hgsc.bcm.edu	37	4	2956258	2956258	+	Missense_Mutation	SNP	C	C	T	rs142398228	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NOP14	NM_003703	exon4	c.G505A	p.G169S	GCCCACCGCCTCC	.	150.0	8.0	46.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
AMDHD1	144193	hgsc.bcm.edu	37	12	96360172	96360172	+	Missense_Mutation	SNP	C	C	A	rs17024904	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	AMDHD1	NM_152435	exon8	c.C1079A	p.P360H	CCATGCCTGAGGC	.	158.0	10.0	59.0	0.0	C|0.977;A|0.023	.	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	98039437	98039437	+	Missense_Mutation	SNP	C	C	T	rs61622928	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DPYD	NM_000110	exon11	c.G1218A	p.M406I	AAACTGCATAGCA	.	359.0	18.0	170.0	0.0	C|0.978;T|0.022	.	Atlas-SNP
SNX1	6642	hgsc.bcm.edu	37	15	64418289	64418289	+	Silent	SNP	A	A	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SNX1	NM_003099	exon6	c.A522T	p.P174P	CTTACCATTGTTC	.	168.0	9.0	69.0	0.0	.	.	Atlas-SNP
NANOGNB	360030	hgsc.bcm.edu	37	12	7922649	7922649	+	Missense_Mutation	SNP	A	A	G	rs114136506	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_001145465	exon2	c.A173G	p.N58S	AACAAAATGGAAA	.	209.0	11.0	85.0	0.0	A|0.996;G|0.004	.	Atlas-SNP
CCDC120	90060	hgsc.bcm.edu	37	X	48923034	48923034	+	Missense_Mutation	SNP	G	G	T	rs144506890	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CCDC120	NM_001163321	exon8	c.G837T	p.K279N	ACCCAAGGCTTGG	.	195.0	15.0	50.0	0.0	G|0.997;T|0.003	.	Atlas-SNP
RNASE6	6039	hgsc.bcm.edu	37	14	21249986	21249986	+	Missense_Mutation	SNP	C	C	T	rs114480851	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RNASE6	NM_005615	exon2	c.C128T	p.P43L	CAAGTCCTCTCCA	.	331.0	14.0	116.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112989772	112989772	+	Silent	SNP	C	C	T	rs139574939	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	BOC	NM_033254	exon6	c.C648T	p.S216S	CTCCAGCGACAGG	.	78.0	6.0	24.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66102224	66102224	+	Silent	SNP	A	A	G	rs6413506	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	LEPR	NM_002303	exon20	c.A3024G	p.S1008S	TAGTTCAGTCACC	.	75.0	12.0	59.0	0.0	A|0.979;G|0.021	.	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232943513	232943513	+	Missense_Mutation	SNP	A	A	T	rs61735509	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	.	NM_019090	exon1	c.A2744T	p.H915L	CTGTACACTCATA	.	143.0	7.0	91.0	0.0	A|0.989;T|0.011	.	Atlas-SNP
DTNBP1	84062	hgsc.bcm.edu	37	6	15523376	15523376	+	Missense_Mutation	SNP	G	G	A	rs74907982	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DTNBP1	NM_032122	exon10	c.C886T	p.P296S	AAGAAGGTGGCTT	.	197.0	8.0	80.0	0.0	G|0.988;A|0.012	.	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47538551	47538551	+	Silent	SNP	C	C	T	rs144482400	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COL6A2	NM_058175	exon13	c.C1140T	p.R380R	AGGACGCAGAGGG	.	135.0	13.0	48.0	0.0	C|0.997;T|0.003	.	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	37	3	73433352	73433352	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PDZRN3	NM_015009	exon10	c.C2365A	p.P789T	TGCTCGGGCAGCT	.	80.0	31.0	22.0	0.0	.	.	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50006026	50006026	+	Missense_Mutation	SNP	G	G	A	rs148635727	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RBM6	NM_005777	exon3	c.G1168A	p.G390S	GAAGGCGGTCTGG	.	149.0	8.0	65.0	0.0	G|0.993;A|0.007	.	Atlas-SNP
APTX	54840	hgsc.bcm.edu	37	9	32987707	32987707	+	Silent	SNP	G	G	A	rs79254654	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	APTX	NM_001195248	exon4	c.C360T	p.N120N	GCCAGGGTTCTTT	.	249.0	13.0	74.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
STX3	6809	hgsc.bcm.edu	37	11	59564795	59564795	+	Missense_Mutation	SNP	G	G	A	rs34563654	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	STX3	NM_004177	exon10	c.G826A	p.G276S	TTGCTGGGCATTT	.	411.0	19.0	183.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23556550	23556550	+	Missense_Mutation	SNP	G	G	A	rs148956643		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF91	NM_003430	exon3	c.C247T	p.P83S	CTGTGGGTTCATC	.	253.0	18.0	64.0	0.0	G|0.992;A|0.008	.	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44980850	44980850	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF180	NM_013256	exon5	c.G1848T	p.Q616H	TGAACTCTGTCTG	.	214.0	84.0	66.0	0.0	.	.	Atlas-SNP
NTRK2	4915	hgsc.bcm.edu	37	9	87366910	87366910	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NTRK2	NM_001018065	exon12	c.G1306C	p.V436L	TATGCTGTGGTGG	.	840.0	37.0	273.0	0.0	.	.	Atlas-SNP
GALNT11	63917	hgsc.bcm.edu	37	7	151800228	151800228	+	Missense_Mutation	SNP	C	C	T	rs6464201	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	GALNT11	NM_022087	exon4	c.C451T	p.P151S	GACCTGCCAGCTG	.	287.0	16.0	106.0	0.0	C|0.961;T|0.039	.	Atlas-SNP
MTHFD2	10797	hgsc.bcm.edu	37	2	74438406	74438406	+	Missense_Mutation	SNP	A	A	G	rs183389698		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MTHFD2	NM_006636	exon6	c.A751G	p.I251V	ATTGTAATATCTG	.	246.0	12.0	92.0	0.0	A|0.980;G|0.020	.	Atlas-SNP
HSPA8	3312	hgsc.bcm.edu	37	11	122929023	122929023	+	Silent	SNP	A	A	G	rs113013616	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HSPA8	NM_006597	exon8	c.T1692C	p.D564D	GTCCTCATCGTTA	.	293.0	15.0	140.0	0.0	A|0.994;G|0.006	.	Atlas-SNP
KLHL13	90293	hgsc.bcm.edu	37	X	117033084	117033084	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	KLHL13	NM_001168299	exon8	c.C1764T	p.F588F	ATTTTCGAAGACA	.	185.0	16.0	79.0	0.0	.	.	Atlas-SNP
CRTAC1	55118	hgsc.bcm.edu	37	10	99655120	99655120	+	Silent	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CRTAC1	NM_001206528	exon11	c.C1368T	p.A456A	GGCAAAGGCCCCA	.	69.0	16.0	17.0	0.0	.	.	Atlas-SNP
MON2	23041	hgsc.bcm.edu	37	12	62902209	62902209	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MON2	NM_015026	exon8	c.G933C	p.M311I	CTGCATGCGTTTG	.	320.0	13.0	144.0	0.0	.	.	Atlas-SNP
ALOX5AP	241	hgsc.bcm.edu	37	13	31309784	31309784	+	Silent	SNP	C	C	T	rs11542984	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ALOX5AP	NM_001204406	exon2	c.C213T	p.I71I	GGCCATCGTCACC	.	106.0	5.0	35.0	0.0	C|0.995;T|0.005	.	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152279962	152279962	+	Missense_Mutation	SNP	C	C	T	rs146768750		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FLG	NM_002016	exon3	c.G7400A	p.G2467E	CTTGACCCCGGGT	.	524.0	23.0	144.0	0.0	C|1.000;T|0.000	.	Atlas-SNP
MT1F	4494	hgsc.bcm.edu	37	16	56691995	56691995	+	Missense_Mutation	SNP	G	G	T	rs76144808	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MT1F	NM_005949	exon1	c.G25T	p.A9S	TGCGCCGCTGGTA	.	159.0	7.0	67.0	0.0	G|0.991;T|0.009	.	Atlas-SNP
VARS	7407	hgsc.bcm.edu	37	6	31760289	31760289	+	Silent	SNP	G	G	A	rs61730575	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	VARS	NM_006295	exon5	c.C666T	p.P222P	AGCCTCGGGGCCT	.	339.0	19.0	129.0	0.0	G|0.991;A|0.009	.	Atlas-SNP
APBB2	323	hgsc.bcm.edu	37	4	41016204	41016204	+	Silent	SNP	C	C	T	rs116718314	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	APBB2	NM_173075	exon6	c.G231A	p.A77A	CATGGCCGCCTGG	.	598.0	29.0	194.0	0.0	C|0.995;T|0.005	.	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214818053	214818053	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	CENPF	NM_016343	exon13	c.G5140A	p.A1714T	ACTGGTGCAGTGA	.	198.0	9.0	105.0	0.0	.	.	Atlas-SNP
SLC1A1	6505	hgsc.bcm.edu	37	9	4561477	4561477	+	Silent	SNP	C	C	T	rs79429045	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC1A1	NM_004170	exon3	c.C261T	p.S87S	CGTATCCGGAAAA	.	272.0	11.0	112.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
SLC26A8	116369	hgsc.bcm.edu	37	6	35919084	35919084	+	Silent	SNP	G	G	A	rs116555814		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC26A8	NM_052961	exon19	c.C2328T	p.D776D	GCCAGCGTCAAAG	.	101.0	36.0	36.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219614067	219614067	+	Missense_Mutation	SNP	G	G	A	rs143759265	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TTLL4	NM_014640	exon14	c.G2692A	p.E898K	CTAGACGAAAACC	.	154.0	8.0	64.0	0.0	G|0.999;A|0.001	.	Atlas-SNP
TAB3	257397	hgsc.bcm.edu	37	X	30872578	30872578	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TAB3	NM_152787	exon6	c.G1204C	p.A402P	TGGTGGCTGTGTA	.	183.0	15.0	91.0	0.0	.	.	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157929357	157929357	+	Missense_Mutation	SNP	A	A	T	rs7456452	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PTPRN2	NM_130843	exon8	c.T1163A	p.L388H	TGGTAAAGTCTAT	.	164.0	7.0	51.0	0.0	A|0.995;T|0.005	.	Atlas-SNP
NPAS3	64067	hgsc.bcm.edu	37	14	34145548	34145548	+	Silent	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	NPAS3	NM_001164749	exon6	c.C690A	p.A230A	CGGAGCCAGCTCA	.	73.0	22.0	16.0	0.0	.	.	Atlas-SNP
MC5R	4161	hgsc.bcm.edu	37	18	13826209	13826209	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	MC5R	NM_005913	exon1	c.C445T	p.R149C	GCCCTGCGCTACC	.	180.0	47.0	79.0	0.0	.	.	Atlas-SNP
DDX24	57062	hgsc.bcm.edu	37	14	94526812	94526812	+	Silent	SNP	C	C	T	rs11845400	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DDX24	NM_020414	exon5	c.G1545A	p.Q515Q	AGGAGCCTGATGC	.	286.0	14.0	148.0	0.0	C|0.952;T|0.048	.	Atlas-SNP
CSRNP3	80034	hgsc.bcm.edu	37	2	166535514	166535514	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	CSRNP3,NS,carcinoma,0	CSRNP3	NM_001172173	exon7	c.G1009T	p.D337Y	GAATTAGATTGCC	.	71.0	25.0	38.0	0.0	.	.	Atlas-SNP
TTC37	9652	hgsc.bcm.edu	37	5	94820541	94820541	+	Missense_Mutation	SNP	C	C	T	rs74664147	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TTC37	NM_014639	exon38	c.G3940A	p.E1314K	ATTTTTCGTCTTT	.	200.0	9.0	86.0	0.0	C|0.998;T|0.002	.	Atlas-SNP
IRX1	79192	hgsc.bcm.edu	37	5	3599680	3599680	+	Silent	SNP	C	C	T	rs61745751	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IRX1	NM_024337	exon2	c.C618T	p.F206F	GCTCTTCGGCAGC	.	160.0	11.0	66.0	0.0	C|0.999;T|0.001	.	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156509699	156509699	+	Silent	SNP	A	A	T	rs77494039	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IQGAP3	NM_178229	exon24	c.T2823A	p.G941G	CTTTAAACCCTTC	.	716.0	30.0	188.0	0.0	A|0.993;T|0.007	.	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70949064	70949064	+	Silent	SNP	A	A	G	rs201952330		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	PTPRB	NM_001109754	exon20	c.T5019C	p.I1673I	CACACGAATGTGT	.	198.0	13.0	44.0	0.0	A|0.999;G|0.000	.	Atlas-SNP
IFT80	57560	hgsc.bcm.edu	37	3	159995248	159995248	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	IFT80	NM_020800	exon18	c.A1945T	p.I649F	AATTGATGTACTG	.	339.0	114.0	160.0	0.0	.	.	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41012182	41012182	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SPTBN4	NM_020971	exon13	c.G1705A	p.E569K	CTGGTGGAGGCAG	.	136.0	26.0	66.0	0.0	.	.	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35434438	35434438	+	Missense_Mutation	SNP	G	G	A	rs8100497	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZNF30	NM_001099438	exon5	c.G571A	p.A191T	GGCTCAGCCTTTG	.	167.0	12.0	77.0	0.0	G|0.985;A|0.015	.	Atlas-SNP
XRRA1	143570	hgsc.bcm.edu	37	11	74559426	74559426	+	Missense_Mutation	SNP	T	T	C	rs12291445	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	XRRA1	NM_182969	exon15	c.A1438G	p.K480E	TATCCTTTGAGGG	.	141.0	9.0	57.0	0.0	T|0.989;C|0.011	.	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40419732	40419732	+	Missense_Mutation	SNP	C	C	T	rs34041323	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	FCGBP	NM_003890	exon6	c.G3262A	p.V1088M	CGCGCACGGCACC	.	103.0	6.0	35.0	0.0	C|0.996;T|0.004	.	Atlas-SNP
SLC20A2	6575	hgsc.bcm.edu	37	8	42295019	42295019	+	Silent	SNP	G	G	T	rs116359869	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLC20A2	NM_001257181	exon8	c.C1011A	p.T337T	GCTCCTGGTGTGG	.	197.0	11.0	83.0	0.0	G|0.980;T|0.020	.	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2130928	2130928	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	POLN	NM_181808	exon16	c.A1845G	p.K615K	GTGGCCTTTGGAT	.	273.0	76.0	132.0	0.0	.	.	Atlas-SNP
HECW1	23072	hgsc.bcm.edu	37	7	43548703	43548703	+	Silent	SNP	A	A	G	rs78404575	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	HECW1	NM_015052	exon24	c.A4002G	p.V1334V	ATTTGTAGAAAAC	.	274.0	14.0	99.0	0.0	A|0.997;G|0.003	.	Atlas-SNP
INO80	54617	hgsc.bcm.edu	37	15	41372055	41372055	+	Silent	SNP	G	G	T	rs34467689	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	INO80	NM_017553	exon9	c.C975A	p.A325A	CTTCTGGGCCTGC	.	179.0	8.0	56.0	0.0	G|0.988;T|0.012	.	Atlas-SNP
TBC1D8B	54885	hgsc.bcm.edu	37	X	106097460	106097460	+	Silent	SNP	T	T	C	rs7886676	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	TBC1D8B	NM_017752	exon14	c.T2286C	p.H762H	TATACATAGTATG	.	262.0	24.0	101.0	0.0	T|0.903;C|0.097	.	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137630361	137630361	+	Silent	SNP	G	G	A	rs61729545	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COL5A1	NM_000093	exon10	c.G1431A	p.A477A	CCCCGCGGTGAGT	.	169.0	9.0	64.0	0.0	G|0.937;A|0.063	.	Atlas-SNP
ATP6V0A1	535	hgsc.bcm.edu	37	17	40650971	40650971	+	Silent	SNP	G	G	A	rs112978072	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ATP6V0A1	NM_001130020	exon15	c.G1611A	p.T537T	ACTGACGTTCTTG	.	506.0	26.0	177.0	0.0	G|0.996;A|0.004	.	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24178738	24178738	+	Missense_Mutation	SNP	G	G	T	rs9314282	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADAM28	NM_014265	exon8	c.G656T	p.R219M	TTAAAAGGTACAA	.	190.0	22.0	125.0	0.0	G|0.961;T|0.039	.	Atlas-SNP
RALGAPA2	57186	hgsc.bcm.edu	37	20	20610175	20610175	+	Silent	SNP	C	C	T	rs6046970		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	RALGAPA2	NM_020343	exon10	c.G1065A	p.T355T	CTGCTCCGTGGGC	.	282.0	12.0	110.0	0.0	C|0.985;T|0.015	.	Atlas-SNP
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32921843	32921843	+	Missense_Mutation	SNP	A	A	G	rs74011135	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ARHGAP11A	NM_199357	exon8	c.A985G	p.T329A	AAGCGTACATTGC	.	437.0	20.0	138.0	0.0	A|0.993;G|0.007	.	Atlas-SNP
ZBTB40	9923	hgsc.bcm.edu	37	1	22817038	22817038	+	Missense_Mutation	SNP	T	T	G	rs147346219	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ZBTB40	NM_001083621	exon3	c.T597G	p.N199K	GAGGAATGCAGAA	.	108.0	9.0	38.0	0.0	T|0.999;G|0.001	.	Atlas-SNP
SMC3	9126	hgsc.bcm.edu	37	10	112350758	112350758	+	Silent	SNP	T	T	C	rs75817442	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SMC3	NM_005445	exon17	c.T1680C	p.Y560Y	ATTTTATCACATT	.	261.0	16.0	147.0	0.0	T|0.995;C|0.005	.	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33749215	33749215	+	Missense_Mutation	SNP	A	A	G	rs140269563	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	SLFN12	NM_018042	exon2	c.T833C	p.M278T	TTCTCCATACAGA	.	203.0	10.0	101.0	0.0	A|0.998;G|0.002	.	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13770941	13770941	+	Silent	SNP	C	C	T	rs35233147	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DNAH5	NM_001369	exon56	c.G9522A	p.T3174T	TTTGGGCGTCACG	.	214.0	10.0	85.0	0.0	C|0.978;T|0.022	.	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139772511	139772511	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	COL22A1	NM_152888	exon18	c.G1877T	p.G626V	GCCACACCAGAAG	.	162.0	111.0	31.0	0.0	.	.	Atlas-SNP
DAB2IP	153090	hgsc.bcm.edu	37	9	124526077	124526077	+	Missense_Mutation	SNP	C	C	T	rs76191175	byfrequency	TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	DAB2IP	NM_032552	exon8	c.C1295T	p.S432L	AGTGCTCGGCCGC	.	145.0	8.0	61.0	0.0	C|0.993;T|0.007	.	Atlas-SNP
ADAD1	132612	hgsc.bcm.edu	37	4	123304976	123304976	+	Silent	SNP	T	T	C	novel		TCGA-BC-A10S-01A-22D-A12Z-10	TCGA-BC-A10S-11A-11D-A16Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	cc8663e0-7310-4ba7-b010-6f66361c2fa0	e82d722e-b10d-43fa-a968-b3378fbb0470	.	ADAD1	NM_139243	exon5	c.T384C	p.F128F	ATATTTTGCCTTT	.	369.0	134.0	165.0	0.0	.	.	Atlas-SNP
