Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	dbSNP_AF	Algorithm
CAMTA1	23261	hgsc.bcm.edu	hg19	1	7151365	7151365	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CAMTA1	NM_015215	exon4	c.A236G	p.E79G	TTCAGGAAATTGC	.	96.0	4.0	78.0	0.0	.	226	.	.	Atlas-SNP
PER3	8863	hgsc.bcm.edu	hg19	1	7887204	7887204	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PER3	NM_016831	exon17	c.T2191C	p.S731P	ACGCGGTCGGCCG	.	95.0	4.0	60.0	0.0	.	95	.	.	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	hg19	1	16174601	16174601	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPEN	NM_015001	exon1	c.A39G	p.L13L	CAACTTACCCGAG	.	97.0	4.0	100.0	0.0	.	374	.	.	Atlas-SNP
SERINC2	347735	hgsc.bcm.edu	hg19	1	31905905	31905905	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SERINC2	NM_001199038	exon10	c.G1132C	p.V378L	CAGCAGGTGGCAG	.	117.0	7.0	82.0	0.0	.	44	.	.	Atlas-SNP
SERINC2	347735	hgsc.bcm.edu	hg19	1	31905906	31905906	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SERINC2	NM_001199038	exon10	c.T1133A	p.V378E	AGCAGGTGGCAGC	.	117.0	6.0	82.0	0.0	.	44	.	.	Atlas-SNP
TRIM62	55223	hgsc.bcm.edu	hg19	1	33646996	33646996	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TRIM62	NM_018207	exon1	c.T38C	p.I13T	AGGCAGATGGAGC	.	43.0	4.0	24.0	0.0	.	26	.	.	Atlas-SNP
GRIK3	2899	hgsc.bcm.edu	hg19	1	37282833	37282833	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GRIK3	NM_000831	exon13	c.G1919T	p.G640V	CAGATGCCACCAA	.	188.0	72.0	127.0	0.0	.	195	.	.	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	hg19	1	52306057	52306057	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NRD1	NM_001101662	exon2	c.T471A	p.D157E	ATCTTCATCATCA	.	263.0	11.0	220.0	0.0	.	89	.	.	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	hg19	1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	rs62648104	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NRD1	NM_001101662	exon2	c.A449T	p.E150V	TCTTCCTCCACCT	.	177.0	14.0	164.0	0.0	.	89	.	T|0.024;A|0.976	Atlas-SNP
DAB1	1600	hgsc.bcm.edu	hg19	1	57480890	57480890	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DAB1	NM_021080	exon14	c.A1110G	p.Q370Q	AACAGTTTGTGTG	.	64.0	5.0	41.0	0.0	.	129	.	.	Atlas-SNP
INADL	10207	hgsc.bcm.edu	hg19	1	62593700	62593700	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	INADL	NM_176877	exon40	c.A5100G	p.G1700G	CTTAGGAGATATC	.	86.0	4.0	62.0	0.0	.	179	.	.	Atlas-SNP
RAVER2	55225	hgsc.bcm.edu	hg19	1	65255125	65255125	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RAVER2	NM_018211	exon5	c.A1033G	p.K345E	ATTATGAAAAGTT	.	80.0	27.0	82.0	0.0	.	56	.	.	Atlas-SNP
FAM73A	374986	hgsc.bcm.edu	hg19	1	78245387	78245387	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FAM73A	NM_001270384	exon1	c.T47C	p.V16A	CTGGCGTGGGCAG	.	90.0	4.0	49.0	0.0	.	56	.	.	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	hg19	1	87025972	87025972	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CLCA4	NM_012128	exon3	c.A379G	p.K127E	GGAGAGAAAGGCG	.	91.0	4.0	52.0	0.0	.	131	.	.	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	hg19	1	87038340	87038340	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CLCA4	NM_012128	exon9	c.C1404T	p.G468G	CAATGGCCTCATT	.	98.0	4.0	109.0	0.0	.	131	.	.	Atlas-SNP
PKN2	5586	hgsc.bcm.edu	hg19	1	89299097	89299097	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PKN2	NM_006256	exon22	c.T2921C	p.F974S	AAATGTTCAGAGA	.	70.0	4.0	69.0	0.0	.	109	.	.	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	hg19	1	103481268	103481268	+	Missense_Mutation	SNP	C	C	A	rs150428394	alternate_allele	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	COL11A1	NM_080629	exon12	c.G1480T	p.A494S	CATCAGCCCCTGG	.	129.0	45.0	134.0	0.0	.	972	.	C|1.000;T|0.000	Atlas-SNP
GPSM2	29899	hgsc.bcm.edu	hg19	1	109465168	109465168	+	Missense_Mutation	SNP	T	T	A	rs201481482		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GPSM2	NM_013296	exon13	c.T1570A	p.S524T	ACAACTTCTTCCA	.	80.0	5.0	53.0	0.0	.	56	.	.	Atlas-SNP
HIPK1	204851	hgsc.bcm.edu	hg19	1	114500750	114500750	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HIPK1	NM_198268	exon8	c.T1818C	p.D606D	TTCAGATGTCTCA	.	136.0	50.0	112.0	0.0	.	195	.	.	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	hg19	1	153907287	153907287	+	Missense_Mutation	SNP	G	G	C	rs199597671		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DENND4B	NM_014856	exon18	c.C2722G	p.Q908E	GCTGCTGCTGCTG	.	80.0	9.0	46.0	0.0	.	210	.	.	Atlas-SNP
HAX1	10456	hgsc.bcm.edu	hg19	1	154247645	154247645	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HAX1	NM_006118	exon5	c.T572C	p.V191A	CCCAGGTTTCCCA	.	91.0	4.0	93.0	0.0	.	25	.	.	Atlas-SNP
EFNA3	1944	hgsc.bcm.edu	hg19	1	155057654	155057654	+	Silent	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EFNA3	NM_004952	exon2	c.C216A	p.G72G	GGTGGGCCCCGGG	.	68.0	10.0	30.0	0.0	.	15	.	.	Atlas-SNP
EFNA3	1944	hgsc.bcm.edu	hg19	1	155057657	155057657	+	Silent	SNP	C	C	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EFNA3	NM_004952	exon2	c.C219G	p.P73P	GGGCCCCGGGGCG	.	72.0	10.0	30.0	0.0	.	15	.	.	Atlas-SNP
MTX1	4580	hgsc.bcm.edu	hg19	1	155180142	155180142	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MTX1	NM_198883	exon2	c.T534C	p.Y178Y	GACCTATGCCAGA	.	119.0	51.0	106.0	0.0	.	17	.	.	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	hg19	1	156622302	156622302	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BCAN	NM_198427	exon8	c.A1560G	p.S520S	TGCATCACCACTT	.	78.0	4.0	48.0	0.0	.	174	.	.	Atlas-SNP
CD48	962	hgsc.bcm.edu	hg19	1	160648863	160648863	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CD48	NM_001778	exon4	c.T711C	p.I237I	GCCAAGAATGGTG	.	85.0	4.0	63.0	0.0	.	31	.	.	Atlas-SNP
FMO3	2328	hgsc.bcm.edu	hg19	1	171061807	171061807	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FMO3	NM_006894	exon2	c.A8G	p.K3R	TGGGGAAGAAAGT	.	98.0	4.0	87.0	0.0	.	73	.	.	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	hg19	1	186276411	186276411	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PRG4,NS,malignant_melanoma,0,1	PRG4	NM_005807	exon7	c.G1560A	p.K520K	TCCCAAGGAGCCT	.	91.0	4.0	79.0	2.0	.	259	.	.	Atlas-SNP
KCNT2	343450	hgsc.bcm.edu	hg19	1	196451495	196451495	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KCNT2	NM_198503	exon4	c.G290C	p.W97S	TTCACCCAAAAGA	.	52.0	19.0	59.0	0.0	.	243	.	.	Atlas-SNP
SOX13	9580	hgsc.bcm.edu	hg19	1	204092852	204092852	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SOX13	NM_005686	exon12	c.T1295C	p.M432T	CCTTCATGGTGTG	.	74.0	4.0	44.0	0.0	.	38	.	.	Atlas-SNP
IARS2	55699	hgsc.bcm.edu	hg19	1	220276069	220276069	+	Silent	SNP	A	A	G	rs112842443		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IARS2	NM_018060	exon7	c.A900G	p.Q300Q	CACACAACCTTGG	.	76.0	4.0	65.0	0.0	.	106	.	A|0.500;G|0.500	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	hg19	1	226016567	226016567	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EPHX1	NM_001136018	exon2	c.A137G	p.D46G	AGGACGACAGCAT	.	99.0	5.0	84.0	0.0	.	57	.	.	Atlas-SNP
LIN9	286826	hgsc.bcm.edu	hg19	1	226420805	226420805	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LIN9	NM_173083	exon14	c.T1563C	p.S521S	GATATTAGAAGCG	.	90.0	4.0	59.0	0.0	.	57	.	.	Atlas-SNP
ADSS	159	hgsc.bcm.edu	hg19	1	244574699	244574699	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ADSS	NM_001126	exon12	c.A1208G	p.K403R	AGAGTCTTATATT	.	89.0	4.0	78.0	0.0	.	49	.	.	Atlas-SNP
CNST	163882	hgsc.bcm.edu	hg19	1	246754974	246754974	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CNST	NM_152609	exon2	c.A110T	p.D37V	CATCAGATGAAAA	.	143.0	45.0	119.0	0.0	.	73	.	.	Atlas-SNP
WDR35	57539	hgsc.bcm.edu	hg19	2	20169327	20169327	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	WDR35,rectum,carcinoma,0,1	WDR35	NM_020779	exon9	c.G922A	p.A308T	ATAGTGCAGATAT	.	47.0	2.0	46.0	0.0	.	92	.	.	Atlas-SNP
NRBP1	29959	hgsc.bcm.edu	hg19	2	27656637	27656637	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NRBP1	NM_013392	exon3	c.A308G	p.E103G	TCTCTGAACGCAA	.	81.0	4.0	74.0	0.0	.	40	.	.	Atlas-SNP
FAM98A	25940	hgsc.bcm.edu	hg19	2	33811687	33811687	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FAM98A	NM_015475	exon6	c.T662C	p.L221P	ATTAGCAGCTTTC	.	87.0	4.0	84.0	0.0	.	42	.	.	Atlas-SNP
RMDN2	151393	hgsc.bcm.edu	hg19	2	38218373	38218373	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_144713	exon7	c.A1412G	p.D471G	ATCTAGATATAGC	.	64.0	4.0	47.0	0.0	.	.	.	.	Atlas-SNP
DYNC2LI1	51626	hgsc.bcm.edu	hg19	2	44032355	44032355	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DYNC2LI1	NM_001193464	exon12	c.A966G	p.E322E	AAATGAAGTCGAT	.	119.0	6.0	99.0	0.0	.	46	.	.	Atlas-SNP
RTN4	57142	hgsc.bcm.edu	hg19	2	55254181	55254181	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RTN4	NM_020532	exon3	c.A1054G	p.K352E	CCAATTTAGTAAG	.	66.0	30.0	84.0	0.0	.	189	.	.	Atlas-SNP
CCDC88A	55704	hgsc.bcm.edu	hg19	2	55562103	55562103	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC88A	NM_018084	exon15	c.A1854G	p.E618E	ATAATGTTCCAAT	.	99.0	4.0	83.0	0.0	.	336	.	.	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	hg19	2	73799567	73799567	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ALMS1	NM_015120	exon16	c.A10560G	p.K3520K	AGACAAACATAGA	.	96.0	4.0	83.0	0.0	.	384	.	.	Atlas-SNP
EIF2AK3	9451	hgsc.bcm.edu	hg19	2	88879055	88879055	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EIF2AK3	NM_004836	exon11	c.A1867G	p.R623G	GGATCCTCTTGAT	.	90.0	5.0	107.0	0.0	.	160	.	.	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	hg19	2	113950141	113950141	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PSD4	NM_012455	exon6	c.G1813A	p.E605K	AAGTCTGAAGTGG	.	33.0	20.0	47.0	0.0	.	74	.	.	Atlas-SNP
NMI	9111	hgsc.bcm.edu	hg19	2	152127280	152127280	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NMI	NM_004688	exon8	c.A851G	p.K284R	CCATTCTTTGCCC	.	94.0	4.0	102.0	0.0	.	21	.	.	Atlas-SNP
NMI	9111	hgsc.bcm.edu	hg19	2	152128184	152128184	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NMI	NM_004688	exon7	c.G697T	p.V233F	CAGTAACTCTATG	.	22.0	14.0	60.0	0.0	.	21	.	.	Atlas-SNP
ACVR1C	130399	hgsc.bcm.edu	hg19	2	158390463	158390463	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	ACVR1C,right_upper_lobe,carcinoma,0,1	ACVR1C	NM_145259	exon9	c.T1449C	p.S483S	AAGTTGAGATATA	.	37.0	2.0	47.0	0.0	.	85	.	.	Atlas-SNP
PLA2R1	22925	hgsc.bcm.edu	hg19	2	160879270	160879270	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLA2R1	NM_001195641	exon7	c.T1200C	p.H400H	AGCCTCATGCCAG	.	81.0	4.0	133.0	0.0	.	153	.	.	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	hg19	2	166788360	166788360	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	TTC21B,NS,carcinoma,0,1	TTC21B	NM_024753	exon8	c.A802G	p.T268A	GCTTGGTGGAAGC	.	55.0	3.0	59.0	0.0	.	130	.	.	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	hg19	2	167142891	167142891	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SCN9A	NM_002977	exon11	c.A1557G	p.E519E	ATGCCCTTCGACA	.	92.0	4.0	127.0	0.0	.	296	.	.	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	hg19	2	167297978	167297978	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SCN7A	NM_002976	exon14	c.C2085T	p.D695D	CATACAGTCCCAC	.	82.0	57.0	146.0	0.0	.	410	.	.	Atlas-SNP
CERS6	253782	hgsc.bcm.edu	hg19	2	169626076	169626076	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_001256126	exon11	c.A1083G	p.E361E	CTCAGAACCTCCG	.	86.0	4.0	59.0	0.0	.	.	.	.	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	hg19	2	170048456	170048456	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LRP2	NM_004525	exon48	c.A8918G	p.D2973G	TCGCCATCACAGA	.	69.0	4.0	78.0	0.0	.	751	.	.	Atlas-SNP
CHN1	1123	hgsc.bcm.edu	hg19	2	175673733	175673733	+	Silent	SNP	T	T	C	rs376051698		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CHN1	NM_001822	exon11	c.A1002G	p.E334E	GATATCTTCATAC	.	93.0	4.0	129.0	0.0	.	67	.	.	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179577610	179577610	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TTN	NM_001267550	exon94	c.T27142A	p.F9048I	CACTGAAAGGAGG	.	95.0	35.0	78.0	0.0	.	18412	.	.	Atlas-SNP
CCDC150	284992	hgsc.bcm.edu	hg19	2	197540964	197540964	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC150	NM_001080539	exon11	c.A1235G	p.N412S	TTCAGAATGAGAA	.	100.0	4.0	120.0	0.0	.	96	.	.	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	hg19	2	203834662	203834662	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ALS2CR8	NM_024744	exon11	c.A974G	p.Q325R	AGGTACAGAAGTT	.	72.0	4.0	112.0	0.0	.	56	.	.	Atlas-SNP
ZDBF2	57683	hgsc.bcm.edu	hg19	2	207174473	207174473	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZDBF2	NM_020923	exon5	c.T5221C	p.C1741R	GTGAGCTGTGAAC	.	72.0	4.0	91.0	0.0	.	531	.	.	Atlas-SNP
FN1	2335	hgsc.bcm.edu	hg19	2	216264012	216264012	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FN1	NM_212476	exon21	c.A3316G	p.T1106A	TCCATGTGATCAC	.	84.0	4.0	78.0	0.0	.	521	.	.	Atlas-SNP
CTDSP1	58190	hgsc.bcm.edu	hg19	2	219266306	219266306	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CTDSP1	NM_001206878	exon2	c.T87C	p.A29A	AGCAGCTTCCCAG	.	87.0	4.0	125.0	0.0	.	19	.	.	Atlas-SNP
MOGAT1	116255	hgsc.bcm.edu	hg19	2	223559205	223559205	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MOGAT1	NM_058165	exon4	c.T603C	p.T201T	GTTCACTCTGTTC	.	57.0	4.0	93.0	0.0	.	47	.	.	Atlas-SNP
LMCD1	29995	hgsc.bcm.edu	hg19	3	8607167	8607167	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LMCD1	NM_014583	exon5	c.A773T	p.Y258F	TGGTCTACTCGGA	.	125.0	51.0	90.0	0.0	.	38	.	.	Atlas-SNP
IQSEC1	9922	hgsc.bcm.edu	hg19	3	12942853	12942853	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IQSEC1	NM_001134382	exon14	c.T2975C	p.L992P	GTGGCCAGGGCTG	.	42.0	5.0	25.0	0.0	.	88	.	.	Atlas-SNP
WNT7A	7476	hgsc.bcm.edu	hg19	3	13896149	13896149	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WNT7A	NM_004625	exon3	c.T450C	p.G150G	GCAGCCACCCCAC	.	63.0	5.0	49.0	0.0	.	70	.	.	Atlas-SNP
METTL6	131965	hgsc.bcm.edu	hg19	3	15467900	15467900	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	METTL6	NM_152396	exon2	c.A119G	p.E40G	TGAGCCTCTTGTT	.	113.0	5.0	84.0	0.0	.	27	.	.	Atlas-SNP
TOP2B	7155	hgsc.bcm.edu	hg19	3	25670532	25670532	+	Silent	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TOP2B	NM_001068	exon14	c.T1779A	p.I593I	CTTTACAATAGGA	.	46.0	23.0	40.0	0.0	.	98	.	.	Atlas-SNP
MYRIP	25924	hgsc.bcm.edu	hg19	3	40211580	40211580	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MYRIP	NM_015460	exon8	c.T869C	p.L290P	CTGCCCTCTGGGT	.	96.0	4.0	58.0	0.0	.	98	.	.	Atlas-SNP
SNRK	54861	hgsc.bcm.edu	hg19	3	43388906	43388906	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SNRK	NM_017719	exon7	c.G1155A	p.A385A	CCACGCGACTGTC	.	47.0	19.0	22.0	0.0	.	118	.	.	Atlas-SNP
KIF15	56992	hgsc.bcm.edu	hg19	3	44816758	44816758	+	Silent	SNP	T	T	C	rs34893204	bycluster;alternate_allele	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KIF15	NM_020242	exon3	c.T75C	p.D25D	AGGTGATGCCATC	.	98.0	4.0	83.0	0.0	.	103	.	T|0.987;A|0.013	Atlas-SNP
CDHR4	389118	hgsc.bcm.edu	hg19	3	49832387	49832387	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CDHR4	NM_001007540	exon9	c.T1178C	p.V393A	TCAAGGACTCTGT	.	73.0	5.0	60.0	0.0	.	37	.	.	Atlas-SNP
NT5DC2	64943	hgsc.bcm.edu	hg19	3	52558487	52558487	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	NT5DC2,bladder,carcinoma,0,1	NT5DC2	NM_001134231	exon14	c.G1673T	p.X558L	TGCCCTCAGCGGA	.	55.0	3.0	47.0	0.0	.	35	.	.	Atlas-SNP
RPP14	11102	hgsc.bcm.edu	hg19	3	58302307	58302307	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RPP14	NM_007042	exon4	c.A228G	p.R76R	CTTGAGAATATGT	.	103.0	5.0	83.0	0.0	.	6	.	.	Atlas-SNP
CADPS	8618	hgsc.bcm.edu	hg19	3	62385129	62385129	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CADPS	NM_003716	exon30	c.G4014A	p.Q1338Q	GATGCCCTGCAGT	.	119.0	45.0	132.0	0.0	.	387	.	.	Atlas-SNP
ADAMTS9	56999	hgsc.bcm.edu	hg19	3	64617541	64617541	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ADAMTS9	NM_182920	exon15	c.G2236C	p.G746R	CGCCACCACAAAC	.	122.0	46.0	104.0	0.0	.	206	.	.	Atlas-SNP
EBLN2	55096	hgsc.bcm.edu	hg19	3	73111481	73111481	+	Missense_Mutation	SNP	C	C	A	rs201649088	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EBLN2	NM_018029	exon1	c.C249A	p.N83K	GAAAAACAGACAG	.	76.0	5.0	64.0	0.0	.	18	.	.	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	hg19	3	73434932	73434932	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PDZRN3	NM_015009	exon9	c.A1523G	p.D508G	CCCTCATCCAGCT	.	78.0	5.0	43.0	0.0	.	196	.	.	Atlas-SNP
SLC35A5	55032	hgsc.bcm.edu	hg19	3	112299917	112299917	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLC35A5	NM_017945	exon6	c.T953C	p.L318P	AGGGCCTTTCAGT	.	90.0	4.0	69.0	0.0	.	40	.	.	Atlas-SNP
GRAMD1C	54762	hgsc.bcm.edu	hg19	3	113601662	113601662	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GRAMD1C	NM_017577	exon6	c.A523G	p.N175D	TGGCAGAATGTAT	.	87.0	4.0	92.0	0.0	.	71	.	.	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	hg19	3	121158914	121158914	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	POLQ	NM_199420	exon27	c.A7314G	p.G2438G	AACAAATCCGTCT	.	30.0	4.0	18.0	0.0	.	273	.	.	Atlas-SNP
MBD4	8930	hgsc.bcm.edu	hg19	3	129151369	129151369	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MBD4	NM_003925	exon7	c.T1642C	p.F548L	CACAAAAAATTCG	.	94.0	4.0	111.0	0.0	.	53	.	.	Atlas-SNP
STAG1	10274	hgsc.bcm.edu	hg19	3	136085882	136085882	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	STAG1	NM_005862	exon25	c.A2588G	p.H863R	CTTTTATGTAAGG	.	149.0	61.0	121.0	0.0	.	135	.	.	Atlas-SNP
ARMC8	25852	hgsc.bcm.edu	hg19	3	137960687	137960687	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ARMC8	NM_213654	exon12	c.A858G	p.G286G	TGAAGGAGCTGAG	.	93.0	4.0	76.0	0.0	.	79	.	.	Atlas-SNP
SLC9A9	285195	hgsc.bcm.edu	hg19	3	143550901	143550901	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLC9A9	NM_173653	exon2	c.A338G	p.H113R	ATGTTGTGCTGAC	.	68.0	4.0	46.0	0.0	.	117	.	.	Atlas-SNP
ZIC1	7545	hgsc.bcm.edu	hg19	3	147128660	147128660	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZIC1	NM_003412	exon1	c.C761A	p.T254K	TAGTTACGCACGT	.	181.0	69.0	103.0	0.0	.	141	.	.	Atlas-SNP
IL12A	3592	hgsc.bcm.edu	hg19	3	159711260	159711260	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IL12A	NM_000882	exon4	c.G401C	p.R134T	ATTCCAGAGAGAC	.	112.0	45.0	115.0	0.0	.	23	.	.	Atlas-SNP
SI	6476	hgsc.bcm.edu	hg19	3	164764772	164764772	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SI	NM_001041	exon16	c.A1744G	p.R582G	AGCTTCTCTTATT	.	142.0	6.0	126.0	0.0	.	500	.	.	Atlas-SNP
PLD1	5337	hgsc.bcm.edu	hg19	3	171406587	171406587	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLD1	NM_002662	exon14	c.C1418T	p.S473L	GCCACCGATTGGT	.	98.0	4.0	83.0	0.0	.	134	.	.	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	hg19	3	172013157	172013157	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	FNDC3B,rectum,carcinoma,0,1	FNDC3B	NM_001135095	exon8	c.C854T	p.S285F	AGGTTTCTAATAT	.	107.0	5.0	107.0	1.0	.	118	.	.	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	hg19	3	183028819	183028819	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MCF2L2	NM_015078	exon10	c.879-2A>G	.	ATAACCTTTCAAG	.	73.0	5.0	66.0	0.0	.	164	.	.	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	hg19	3	184646287	184646287	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VPS8	NM_001009921	exon31	c.A2680G	p.S894G	GAAGAGAGTCGAC	.	92.0	4.0	61.0	0.0	.	109	.	.	Atlas-SNP
SEPSECS	51091	hgsc.bcm.edu	hg19	4	25160704	25160704	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	SEPSECS_ENST00000382103,NS,carcinoma,0,2	SEPSECS	NM_016955	exon2	c.A140G	p.D47G	CTTTCATCCCAGC	.	84.0	6.0	57.0	1.0	.	55	.	.	Atlas-SNP
RFC1	5981	hgsc.bcm.edu	hg19	4	39352986	39352986	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RFC1	NM_002913	exon2	c.A114G	p.K38K	TATTCCTTTCTTT	.	70.0	4.0	73.0	0.0	.	114	.	.	Atlas-SNP
GNPDA2	132789	hgsc.bcm.edu	hg19	4	44709828	44709828	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GNPDA2	NM_138335	exon6	c.T710C	p.F237S	CATACAAAAATAG	.	89.0	4.0	74.0	0.0	.	28	.	.	Atlas-SNP
PROL1	58503	hgsc.bcm.edu	hg19	4	71275489	71275489	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PROL1,NS,carcinoma,0,1	PROL1	NM_021225	exon3	c.C444T	p.T148T	CACCACCGCAGAT	.	134.0	91.0	174.0	0.0	.	46	.	.	Atlas-SNP
RUFY3	22902	hgsc.bcm.edu	hg19	4	71588361	71588361	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RUFY3	NM_001037442	exon1	c.A71G	p.E24G	CCATGGAGACCAT	.	98.0	4.0	86.0	0.0	.	61	.	.	Atlas-SNP
SLC4A4	8671	hgsc.bcm.edu	hg19	4	72306489	72306489	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLC4A4	NM_001098484	exon8	c.A964G	p.R322G	CCCACAAGGTAAG	.	99.0	4.0	133.0	0.0	.	269	.	.	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	hg19	4	77247091	77247091	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC158	NM_001042784	exon22	c.A3076G	p.T1026A	AACTAGTTAGGAG	.	80.0	4.0	60.0	0.0	.	114	.	.	Atlas-SNP
CCDC158	339965	hgsc.bcm.edu	hg19	4	77324342	77324342	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	CCDC158,NS,carcinoma,0,1	CCDC158	NM_001042784	exon2	c.G19A	p.E7K	TTGATTCCCAAGC	.	44.0	2.0	55.0	0.0	.	114	.	.	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	hg19	4	88411956	88411956	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPARCL1	NM_004684	exon6	c.T1366C	p.C456R	CCTGGCAGACACA	.	98.0	4.0	155.0	0.0	.	59	.	.	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	hg19	4	88535745	88535745	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DSPP	NM_014208	exon5	c.A1931G	p.D644G	GCAGTGACAGCAA	.	110.0	6.0	159.0	0.0	.	174	.	.	Atlas-SNP
EMCN	51705	hgsc.bcm.edu	hg19	4	101396223	101396223	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EMCN	NM_001159694	exon3	c.A231G	p.T77T	AGTAGCTGTTGAC	.	38.0	4.0	56.0	0.0	.	37	.	.	Atlas-SNP
NFKB1	4790	hgsc.bcm.edu	hg19	4	103531782	103531782	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NFKB1	NM_003998	exon20	c.T2278C	p.S760P	GATGACTCTTGGG	.	46.0	4.0	77.0	0.0	.	78	.	.	Atlas-SNP
BDH2	56898	hgsc.bcm.edu	hg19	4	104013835	104013835	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BDH2	NM_020139	exon4	c.T170C	p.L57P	ACATCAAGGACAC	.	135.0	6.0	199.0	0.0	.	18	.	.	Atlas-SNP
GAR1	54433	hgsc.bcm.edu	hg19	4	110739158	110739158	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GAR1	NM_018983	exon3	c.A281G	p.K94R	AAAATAAGGTGCC	.	49.0	4.0	71.0	0.0	.	16	.	.	Atlas-SNP
AP1AR	55435	hgsc.bcm.edu	hg19	4	113187842	113187842	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AP1AR	NM_018569	exon9	c.T613C	p.S205P	AGCACATCCTTAG	.	92.0	4.0	125.0	0.0	.	25	.	.	Atlas-SNP
MYOZ2	51778	hgsc.bcm.edu	hg19	4	120079180	120079180	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	MYOZ2,NS,carcinoma,0,1	MYOZ2	NM_016599	exon4	c.A250G	p.S84G	CAGCACAGTATTG	.	38.0	2.0	59.0	1.0	.	34	.	.	Atlas-SNP
PHF17	79960	hgsc.bcm.edu	hg19	4	129792723	129792723	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PHF17	NM_199320	exon11	c.T1835C	p.L612P	CCCTGCTGAAGCA	.	73.0	4.0	81.0	0.0	.	63	.	.	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	hg19	4	143067030	143067030	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	INPP4B	NM_003866	exon19	c.A1683G	p.E561E	TGAAGGTTCCTTT	.	91.0	4.0	107.0	0.0	.	132	.	.	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	hg19	4	148559746	148559746	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PRMT10,NS,carcinoma,0,1	PRMT10	NM_138364	exon12	c.A2475G	p.G825G	TTCCTCTCCCATT	.	100.0	4.0	129.0	0.0	.	68	.	.	Atlas-SNP
RXFP1	59350	hgsc.bcm.edu	hg19	4	159526291	159526291	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RXFP1	NM_001253727	exon5	c.T545C	p.L182P	AGAAGCTGTAAGA	.	89.0	5.0	133.0	0.0	.	98	.	.	Atlas-SNP
CPE	1363	hgsc.bcm.edu	hg19	4	166418679	166418679	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	CPE,NS,carcinoma,0,1	CPE	NM_001873	exon9	c.G1348A	p.E450K	GAACTGGAGTCAT	.	28.0	2.0	47.0	0.0	.	65	.	.	Atlas-SNP
FAM105A	54491	hgsc.bcm.edu	hg19	5	14609107	14609107	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	FAM105A,caecum,carcinoma,0,1	FAM105A	NM_019018	exon7	c.A878G	p.D293G	TAGGCGACACATG	.	87.0	4.0	88.0	0.0	.	32	.	.	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	hg19	5	35628606	35628606	+	Nonsense_Mutation	SNP	G	G	T	rs78964548	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPEF2	NM_024867	exon2	c.G103T	p.G35X	CTACTTGGAGAAG	.	92.0	4.0	94.0	0.0	.	324	.	.	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	hg19	5	35792503	35792503	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPEF2	NM_024867	exon31	c.C4509T	p.G1503G	CCTTGGCACAAAC	.	89.0	4.0	70.0	0.0	.	324	.	.	Atlas-SNP
NADKD1	133686	hgsc.bcm.edu	hg19	5	36219720	36219720	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	NADKD1,NS,carcinoma,0,1	NADKD1	NM_001085411	exon5	c.A622G	p.K208E	AGAACTTCTGTAA	.	50.0	2.0	32.0	0.0	.	47	.	.	Atlas-SNP
NIPBL	25836	hgsc.bcm.edu	hg19	5	36984922	36984922	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NIPBL	NM_015384	exon10	c.A1640G	p.Q547R	TTCATCAGGCAGG	.	100.0	4.0	57.0	0.0	.	513	.	.	Atlas-SNP
HCN1	348980	hgsc.bcm.edu	hg19	5	45303811	45303811	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HCN1	NM_021072	exon6	c.T1508C	p.I503T	TCTCGTATGATAT	.	131.0	55.0	114.0	0.0	.	298	.	.	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	hg19	5	56178549	56178549	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MAP3K1	NM_005921	exon14	c.T3522C	p.N1174N	TCATAATCAAAAG	.	94.0	4.0	98.0	0.0	.	355	.	.	Atlas-SNP
KIF2A	3796	hgsc.bcm.edu	hg19	5	61669513	61669513	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KIF2A	NM_001098511	exon18	c.1761-1G>A	.	TTTATAGGGTCAA	.	85.0	40.0	63.0	0.0	.	69	.	.	Atlas-SNP
AP3B1	8546	hgsc.bcm.edu	hg19	5	77471657	77471657	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AP3B1	NM_003664	exon10	c.T1046C	p.V349A	TACTGCACCTCCC	.	85.0	4.0	60.0	0.0	.	94	.	.	Atlas-SNP
RASA1	5921	hgsc.bcm.edu	hg19	5	86682657	86682657	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	RASA1_ENST00000456692,NS,carcinoma,0,2	RASA1	NM_002890	exon23	c.A2862G	p.E954E	CATGGAAGGTGTC	.	62.0	4.0	66.0	0.0	.	213	.	.	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	hg19	5	112874844	112874844	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	YTHDC2	NM_022828	exon8	c.A1176G	p.K392K	AAACAAAGAAATG	.	63.0	4.0	55.0	0.0	.	118	.	.	Atlas-SNP
PRRC1	133619	hgsc.bcm.edu	hg19	5	126859184	126859184	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PRRC1	NM_130809	exon2	c.A13G	p.S5G	GAAGAGAGTGGAA	.	67.0	4.0	67.0	0.0	.	22	.	.	Atlas-SNP
FAM13B	51306	hgsc.bcm.edu	hg19	5	137354156	137354156	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FAM13B	NM_001101800	exon4	c.A205G	p.T69A	CCACTGTCTCAGC	.	97.0	4.0	95.0	0.0	.	46	.	.	Atlas-SNP
CDC23	8697	hgsc.bcm.edu	hg19	5	137537070	137537070	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CDC23	NM_004661	exon5	c.A483G	p.K161K	TTGGTGTTTTTTG	.	72.0	4.0	75.0	0.0	.	46	.	.	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	hg19	5	140724262	140724262	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PCDHGA3	NM_032011	exon1	c.T662C	p.V221A	ACCCTGTCCACTC	.	95.0	4.0	74.0	0.0	.	246	.	.	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	hg19	5	140803211	140803211	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PCDHGA11	NM_032091	exon1	c.A2417G	p.D806G	AATGTGACCCGAC	.	84.0	5.0	98.0	0.0	.	128	.	.	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	hg19	5	141024179	141024179	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FCHSD1	NM_033449	exon16	c.A1603G	p.S535G	CTTGGCTGCTCTC	.	82.0	4.0	69.0	0.0	.	51	.	.	Atlas-SNP
CYFIP2	26999	hgsc.bcm.edu	hg19	5	156721863	156721863	+	Silent	SNP	T	T	C	rs200051515		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CYFIP2	NM_001037332	exon4	c.T279C	p.I93I	GGCCATTCCCAGG	.	199.0	9.0	185.0	0.0	.	354	.	.	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	hg19	5	167871522	167871522	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WWC1	NM_015238	exon17	c.A2457G	p.E819E	GTTGGAACAGACA	.	96.0	4.0	89.0	0.0	.	98	.	.	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	hg19	5	170610408	170610408	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RANBP17	NM_022897	exon18	c.T2012C	p.L671P	CAGCGCTCACTCG	.	98.0	4.0	88.0	0.0	.	108	.	.	Atlas-SNP
TXNDC5	81567	hgsc.bcm.edu	hg19	6	7884705	7884705	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TXNDC5	NM_030810	exon9	c.A1063G	p.T355A	CCAGAGTCTTACA	.	82.0	4.0	49.0	0.0	.	33	.	.	Atlas-SNP
NFKBIL1	4795	hgsc.bcm.edu	hg19	6	31525591	31525591	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NFKBIL1	NM_005007	exon3	c.A521G	p.E174G	AGCTGGAGGACGA	.	94.0	4.0	60.0	0.0	.	17	.	.	Atlas-SNP
HSPA1L	3305	hgsc.bcm.edu	hg19	6	31778417	31778417	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HSPA1L	NM_005527	exon2	c.T1333C	p.Y445H	CCTCATACACCTG	.	365.0	118.0	239.0	0.0	.	185	.	.	Atlas-SNP
SLC44A4	80736	hgsc.bcm.edu	hg19	6	31833556	31833556	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	SLC44A4,NS,NS,0,1	SLC44A4	NM_025257	exon15	c.A1493G	p.H498R	CCAGTGTGGTAAC	.	41.0	2.0	26.0	0.0	.	67	.	.	Atlas-SNP
BRD2	6046	hgsc.bcm.edu	hg19	6	32946061	32946061	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BRD2	NM_005104	exon10	c.C1737T	p.P579P	GGCACCCCGCCCA	.	98.0	4.0	60.0	0.0	.	70	.	.	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	hg19	6	42227243	42227243	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TRERF1	NM_033502	exon9	c.C2103A	p.P701P	GTGGGTGGGGTCC	.	158.0	60.0	61.0	0.0	.	124	.	.	Atlas-SNP
KLC4	89953	hgsc.bcm.edu	hg19	6	43039095	43039095	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KLC4	NM_201523	exon9	c.A1292G	p.E431G	TACAGGAGTTTGG	.	106.0	5.0	79.0	0.0	.	89	.	.	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	hg19	6	90661469	90661469	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BACH2	NM_001170794	exon5	c.A356G	p.H119R	AGGTTGTGCATGC	.	95.0	4.0	105.0	0.0	.	224	.	.	Atlas-SNP
FAM184A	79632	hgsc.bcm.edu	hg19	6	119324140	119324140	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	FAM184A,NS,carcinoma,0,1	FAM184A	NM_024581	exon9	c.T2012C	p.L671P	TGCAAAAGTTGAG	.	40.0	2.0	54.0	0.0	.	109	.	.	Atlas-SNP
TBPL1	9519	hgsc.bcm.edu	hg19	6	134305776	134305776	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TBPL1	NM_004865	exon6	c.C448T	p.Q150X	ACATTACAGATTT	.	84.0	4.0	159.0	0.0	.	20	.	.	Atlas-SNP
IFNGR1	3459	hgsc.bcm.edu	hg19	6	137540422	137540422	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IFNGR1	NM_000416	exon1	c.A43G	p.S15G	CCCTGCTCACACC	.	98.0	5.0	104.0	0.0	.	46	.	.	Atlas-SNP
ARID1B	57492	hgsc.bcm.edu	hg19	6	157256613	157256613	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ARID1B	NM_020732	exon5	c.A1940G	p.E647G	CTCAGGAAGGCTA	.	73.0	4.0	99.0	0.0	.	320	.	.	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	hg19	7	4794874	4794874	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FOXK1	NM_001037165	exon4	c.T910C	p.S304P	GATGAGTCAAAGC	.	59.0	4.0	42.0	0.0	.	64	.	.	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	hg19	7	4899811	4899811	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PAPOLB	NM_020144	exon1	c.A1631G	p.K544R	CCTGTCTTCATAG	.	77.0	4.0	69.0	0.0	.	93	.	.	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	hg19	7	5355649	5355649	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TNRC18	NM_001080495	exon25	c.G6800C	p.G2267A	GTGTCTCCGTCGT	.	66.0	27.0	65.0	0.0	.	311	.	.	Atlas-SNP
SP8	221833	hgsc.bcm.edu	hg19	7	20824956	20824956	+	Silent	SNP	C	C	G	rs201180283		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SP8	NM_182700	exon2	c.G480C	p.G160G	GCCGCCCCCGCCG	.	10.0	6.0	2.0	0.0	.	43	.	.	Atlas-SNP
KLHL7	55975	hgsc.bcm.edu	hg19	7	23145743	23145743	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KLHL7	NM_001172428	exon1	c.T98C	p.V33A	TGGGCGTCATGAA	.	52.0	4.0	59.0	0.0	.	102	.	.	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	hg19	7	30821784	30821784	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FAM188B	NM_032222	exon3	c.A375G	p.E125E	AGATGAAGATGCA	.	77.0	4.0	49.0	0.0	.	62	.	.	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	hg19	7	32609744	32609744	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AVL9	NM_015060	exon11	c.A1328G	p.H443R	AGAAACACCTCAG	.	123.0	5.0	91.0	0.0	.	66	.	.	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	hg19	7	47873952	47873952	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PKD1L1	NM_138295	exon40	c.A6159G	p.A2053A	CTCCTGTGCGTCT	.	73.0	4.0	77.0	0.0	.	328	.	.	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	hg19	7	55466298	55466298	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LANCL2	NM_018697	exon3	c.T505C	p.C169R	AGTGACTGTGAGT	.	82.0	4.0	88.0	0.0	.	54	.	.	Atlas-SNP
ZNF117	51351	hgsc.bcm.edu	hg19	7	64439846	64439846	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZNF117	NM_015852	exon4	c.A103G	p.T35A	TTAGGGTCACTTT	.	60.0	4.0	68.0	0.0	.	56	.	.	Atlas-SNP
FKBP6	8468	hgsc.bcm.edu	hg19	7	72744311	72744311	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FKBP6	NM_003602	exon4	c.T424C	p.F142L	CTTGACTTCCTGG	.	117.0	6.0	69.0	0.0	.	35	.	.	Atlas-SNP
HGF	3082	hgsc.bcm.edu	hg19	7	81358964	81358964	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HGF	NM_000601	exon8	c.T997C	p.Y333H	GAGGATACTGAGA	.	83.0	5.0	60.0	0.0	.	171	.	.	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	hg19	7	97873966	97873966	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TECPR1	NM_015395	exon5	c.A448G	p.K150E	TGTCTTTCGTGTA	.	75.0	4.0	56.0	0.0	.	77	.	.	Atlas-SNP
TMEM130	222865	hgsc.bcm.edu	hg19	7	98460878	98460878	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TMEM130	NM_152913	exon2	c.C231A	p.T77T	CAGCGGGGTGTGG	.	94.0	39.0	74.0	0.0	.	54	.	.	Atlas-SNP
C7orf43	55262	hgsc.bcm.edu	hg19	7	99755336	99755336	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	C7orf43	NM_018275	exon3	c.A557G	p.D186G	CCTTGATCTCTGA	.	95.0	4.0	62.0	0.0	.	28	.	.	Atlas-SNP
MLL5	55904	hgsc.bcm.edu	hg19	7	104717613	104717613	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MLL5	NM_018682	exon9	c.C972T	p.N324N	TACCAACAATTTG	.	97.0	4.0	65.0	0.0	.	173	.	.	Atlas-SNP
TMEM168	64418	hgsc.bcm.edu	hg19	7	112423763	112423763	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TMEM168	NM_022484	exon2	c.T1118C	p.V373A	CAGGAAACTGCTC	.	75.0	4.0	33.0	0.0	.	84	.	.	Atlas-SNP
ING3	54556	hgsc.bcm.edu	hg19	7	120607623	120607623	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ING3	NM_019071	exon7	c.T477C	p.D159D	AACAGATCATATT	.	87.0	4.0	54.0	0.0	.	36	.	.	Atlas-SNP
CREB3L2	64764	hgsc.bcm.edu	hg19	7	137612918	137612918	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CREB3L2	NM_001253775	exon2	c.C297T	p.T99T	ACTGGTGGTAATG	.	360.0	23.0	186.0	0.0	.	62	.	.	Atlas-SNP
AKR1D1	6718	hgsc.bcm.edu	hg19	7	137782670	137782670	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AKR1D1	NM_001190907	exon4	c.A437G	p.N146S	AGTCAAATCTGTG	.	52.0	4.0	29.0	0.0	.	52	.	.	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149489269	149489269	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_198455	exon36	c.A5514G	p.P1838P	GTGCCCACCTGAT	.	99.0	4.0	42.0	0.0	.	.	.	.	Atlas-SNP
NEFL	4747	hgsc.bcm.edu	hg19	8	24811079	24811079	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NEFL	NM_006158	exon3	c.A1400T	p.K467M	TCATCCTTGGCTT	.	30.0	24.0	52.0	0.0	.	47	.	.	Atlas-SNP
IDO1	3620	hgsc.bcm.edu	hg19	8	39776332	39776332	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IDO1	NM_002164	exon4	c.304-2A>G	.	TTAATCAGGTCTT	.	60.0	4.0	71.0	0.0	.	43	.	.	Atlas-SNP
PPP1R42	286187	hgsc.bcm.edu	hg19	8	67900622	67900622	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PPP1R42	NM_001013626	exon6	c.A683G	p.Y228C	TATTAATATAAAT	.	19.0	10.0	3.0	0.0	.	2	.	.	Atlas-SNP
KCNB2	9312	hgsc.bcm.edu	hg19	8	73849087	73849087	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KCNB2	NM_004770	exon3	c.G1497A	p.L499L	GGCTCTGTCGGAA	.	48.0	12.0	17.0	0.0	.	228	.	.	Atlas-SNP
RNF19A	25897	hgsc.bcm.edu	hg19	8	101271049	101271049	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RNF19A	NM_015435	exon11	c.A2252G	p.H751R	CGGGTGTGATAAT	.	99.0	4.0	70.0	0.0	.	67	.	.	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	hg19	8	103300480	103300480	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	UBR5	NM_015902	exon36	c.G4728A	p.E1576E	CACACCCTCCACC	.	141.0	35.0	75.0	0.0	.	285	.	.	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	hg19	8	110457871	110457871	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PKHD1L1	NM_177531	exon38	c.A5773G	p.R1925G	CCAAGCAGAGGTA	.	84.0	30.0	52.0	0.0	.	522	.	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	hg19	8	113331087	113331087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	CSMD3_ENST00000343508,NS,malignant_melanoma,0,2	CSMD3	NM_198123	exon47	c.G7339A	p.G2447R	GTGCTCCATCCAT	.	39.0	2.0	26.0	0.0	.	2325	.	.	Atlas-SNP
TRPS1	7227	hgsc.bcm.edu	hg19	8	116430680	116430680	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TRPS1	NM_014112	exon6	c.A2701G	p.R901G	TACGCCTCTGAAA	.	114.0	5.0	104.0	0.0	.	516	.	.	Atlas-SNP
DERL1	79139	hgsc.bcm.edu	hg19	8	124037286	124037286	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DERL1	NM_001134671	exon3	c.T270C	p.A90A	ATCAAAAGCTCCT	.	61.0	4.0	37.0	0.0	.	27	.	.	Atlas-SNP
KCNK9	51305	hgsc.bcm.edu	hg19	8	140631049	140631049	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KCNK9	NM_016601	exon2	c.T577C	p.C193R	TGAAGCAGTAGTA	.	141.0	46.0	87.0	0.0	.	100	.	.	Atlas-SNP
SLURP1	57152	hgsc.bcm.edu	hg19	8	143823269	143823269	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLURP1	NM_020427	exon2	c.A130G	p.K44E	CTGGCTTGCAGCG	.	100.0	4.0	43.0	0.0	.	16	.	.	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	hg19	8	144940614	144940614	+	Missense_Mutation	SNP	C	C	T	rs200821582	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	EPPK1,NS,carcinoma,0,1	EPPK1	NM_031308	exon1	c.G6808A	p.G2270S	CGAAGCCGGTGGC	.	20.0	8.0	3.0	1.0	.	199	.	C|0.998;T|0.002	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	hg19	8	144944633	144944633	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EPPK1	NM_031308	exon1	c.G2789A	p.G930E	ACAGCTCCCAGGC	.	35.0	12.0	14.0	0.0	.	199	.	.	Atlas-SNP
PLAA	9373	hgsc.bcm.edu	hg19	9	26905635	26905635	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLAA	NM_001031689	exon14	c.T2262C	p.S754S	ATCATCACTGATA	.	76.0	4.0	103.0	0.0	.	48	.	.	Atlas-SNP
FANCG	2189	hgsc.bcm.edu	hg19	9	35077012	35077012	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FANCG	NM_004629	exon6	c.T733C	p.L245L	GGACCAACACAGG	.	93.0	4.0	83.0	0.0	.	56	.	.	Atlas-SNP
CCIN	881	hgsc.bcm.edu	hg19	9	36169807	36169807	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCIN	NM_005893	exon1	c.A308T	p.E103V	TGGAGGAGCTGCT	.	126.0	46.0	104.0	0.0	.	56	.	.	Atlas-SNP
C9orf85	138241	hgsc.bcm.edu	hg19	9	74561974	74561974	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	C9orf85	NM_182505	exon2	c.T155C	p.L52P	AAGTTCTTGAGTG	.	81.0	4.0	61.0	0.0	.	28	.	.	Atlas-SNP
PHF2	5253	hgsc.bcm.edu	hg19	9	96438992	96438992	+	Silent	SNP	A	A	T	rs10821200	by2hit2allele;alternate_allele	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PHF2,caecum,carcinoma,0,1	PHF2	NM_005392	exon21	c.A2949T	p.P983P	CACGCCAGCCTCT	.	43.0	6.0	23.0	1.0	.	113	.	.	Atlas-SNP
TDRD7	23424	hgsc.bcm.edu	hg19	9	100222509	100222509	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TDRD7	NM_014290	exon7	c.A905G	p.K302R	CAGCTAAGAGAAA	.	96.0	4.0	100.0	0.0	.	78	.	.	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	hg19	9	101544811	101544811	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ANKS6	NM_173551	exon5	c.T1157C	p.V386A	AGAGTGACATCGG	.	90.0	4.0	81.0	0.0	.	59	.	.	Atlas-SNP
LCN2	3934	hgsc.bcm.edu	hg19	9	130911936	130911936	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LCN2	NM_005564	exon1	c.C132A	p.D44E	CCAGGACAACCAA	.	75.0	29.0	68.0	0.0	.	12	.	.	Atlas-SNP
GTF3C4	9329	hgsc.bcm.edu	hg19	9	135562687	135562687	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GTF3C4	NM_012204	exon4	c.A2377G	p.S793G	CATGACAGCATTG	.	78.0	4.0	76.0	0.0	.	53	.	.	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	hg19	9	136578161	136578161	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SARDH	NM_007101	exon9	c.A1236G	p.A412A	CTCACCTGCGCTG	.	41.0	15.0	26.0	0.0	.	112	.	.	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	hg19	9	139306975	139306975	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PMPCA	NM_015160	exon3	c.A308G	p.K103R	AAGCGAAATACCT	.	94.0	4.0	82.0	0.0	.	29	.	.	Atlas-SNP
CCDC3	83643	hgsc.bcm.edu	hg19	10	13040436	13040436	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC3	NM_031455	exon2	c.A451G	p.R151G	TCCTTCTGTTCTC	.	94.0	26.0	83.0	0.0	.	27	.	.	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	hg19	10	26442791	26442791	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MYO3A	NM_017433	exon24	c.A2648T	p.H883L	TGCCACATTCTAA	.	142.0	6.0	140.0	0.0	.	371	.	.	Atlas-SNP
ANKRD26	22852	hgsc.bcm.edu	hg19	10	27349321	27349321	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ANKRD26	NM_014915	exon15	c.T1517C	p.V506A	TTTGGAACAGAAT	.	124.0	5.0	88.0	0.0	.	179	.	.	Atlas-SNP
KIAA1462	57608	hgsc.bcm.edu	hg19	10	30317392	30317392	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KIAA1462	NM_020848	exon3	c.A1685G	p.Q562R	CCAGTTTGGAACT	.	40.0	4.0	24.0	0.0	.	162	.	.	Atlas-SNP
EPC1	80314	hgsc.bcm.edu	hg19	10	32576101	32576101	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EPC1	NM_025209	exon7	c.T1077C	p.A359A	CAGTGCAGCAGGA	.	71.0	4.0	48.0	0.0	.	74	.	.	Atlas-SNP
ANK3	288	hgsc.bcm.edu	hg19	10	61874003	61874003	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	ANK3_ENST00000395293,NS,carcinoma,0,3	ANK3	NM_001204404	exon27	c.T2931C	p.V977V	GCTTGAAACAAGA	.	44.0	2.0	45.0	0.0	.	703	.	.	Atlas-SNP
MYPN	84665	hgsc.bcm.edu	hg19	10	69918260	69918260	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MYPN	NM_032578	exon7	c.A1335G	p.S445S	TTTGTCAGCTTCT	.	89.0	4.0	61.0	0.0	.	189	.	.	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	hg19	10	75058853	75058853	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TTC18	NM_145170	exon15	c.A1534G	p.S512G	AGTCACTCACTGC	.	85.0	4.0	55.0	0.0	.	106	.	.	Atlas-SNP
RGR	5995	hgsc.bcm.edu	hg19	10	86018358	86018358	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RGR	NM_002921	exon7	c.T851C	p.L284P	AGTGCCTCTCACC	.	117.0	5.0	65.0	0.0	.	42	.	.	Atlas-SNP
PTEN	5728	hgsc.bcm.edu	hg19	10	89653817	89653817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PTEN,colon,carcinoma,-2,1	PTEN	NM_000314	exon2	c.G115A	p.A39T	TTTCCTGCAGAAA	.	88.0	4.0	66.0	1.0	.	3652	.	.	Atlas-SNP
MARCH5	54708	hgsc.bcm.edu	hg19	10	94109142	94109142	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MARCH5	NM_017824	exon4	c.A406G	p.R136G	ATGGAGAGAGCTG	.	97.0	4.0	87.0	0.0	.	28	.	.	Atlas-SNP
SMC3	9126	hgsc.bcm.edu	hg19	10	112338437	112338437	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SMC3	NM_005445	exon7	c.T402C	p.N134N	AAGCAATCCTTAT	.	55.0	4.0	51.0	0.0	.	103	.	.	Atlas-SNP
PLEKHS1	79949	hgsc.bcm.edu	hg19	10	115515016	115515016	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLEKHS1	.	.	.	.	TTTGACAGGGGAG	.	65.0	4.0	64.0	0.0	.	19	.	.	Atlas-SNP
FAM160B1	57700	hgsc.bcm.edu	hg19	10	116605202	116605202	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FAM160B1	NM_020940	exon8	c.T1090C	p.F364L	TCCTGGTTTGATT	.	80.0	4.0	78.0	0.0	.	107	.	.	Atlas-SNP
HMX2	3167	hgsc.bcm.edu	hg19	10	124909334	124909334	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HMX2	NM_005519	exon2	c.T517C	p.Y173H	AAGCGCTACCTGA	.	82.0	37.0	66.0	0.0	.	21	.	.	Atlas-SNP
AP2A2	161	hgsc.bcm.edu	hg19	11	992671	992671	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AP2A2	NM_001242837	exon11	c.A1441T	p.K481X	GCGGCCAAGACTG	.	155.0	65.0	118.0	0.0	.	50	.	.	Atlas-SNP
OR51I2	390064	hgsc.bcm.edu	hg19	11	5475431	5475431	+	Missense_Mutation	SNP	T	T	A	rs199654892	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OR51I2	NM_001004754	exon1	c.T713A	p.L238H	AAGCTCTCAACAC	.	230.0	14.0	206.0	0.0	.	76	.	.	Atlas-SNP
LDHA	3939	hgsc.bcm.edu	hg19	11	18425285	18425285	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LDHA	NM_001165414	exon6	c.A724G	p.T242A	CTGAAGACTCTGC	.	68.0	5.0	64.0	0.0	.	118	.	.	Atlas-SNP
SYT13	57586	hgsc.bcm.edu	hg19	11	45307751	45307751	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SYT13	NM_020826	exon1	c.T8C	p.L3P	ACCGACAGCACCA	.	61.0	4.0	24.0	0.0	.	45	.	.	Atlas-SNP
CKAP5	9793	hgsc.bcm.edu	hg19	11	46819406	46819406	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CKAP5	NM_001008938	exon11	c.T1287C	p.A429A	GGTAGAAGCAGTG	.	100.0	4.0	69.0	0.0	.	134	.	.	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	hg19	11	47788670	47788670	+	Silent	SNP	G	G	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FNBP4	NM_015308	exon1	c.C171G	p.T57T	GGTGGTGGTGGTC	.	7.0	5.0	0.0	0.0	.	99	.	.	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	hg19	11	55579735	55579735	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OR5L1	NM_001004738	exon1	c.G793T	p.G265C	AGTTCAGGCAATA	.	82.0	34.0	58.0	0.0	.	145	.	.	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	hg19	11	55579736	55579736	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OR5L1	NM_001004738	exon1	c.G794T	p.G265V	GTTCAGGCAATAG	.	82.0	34.0	60.0	0.0	.	145	.	.	Atlas-SNP
MS4A6A	64231	hgsc.bcm.edu	hg19	11	59947440	59947440	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MS4A6A	NM_152851	exon4	c.148-2A>G	.	ATAGTCTGTGGGA	.	89.0	4.0	88.0	0.0	.	85	.	.	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	hg19	11	61906200	61906200	+	Silent	SNP	A	A	G	rs150865728		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	INCENP	NM_001040694	exon6	c.A1131G	p.E377E	GAAGGAACCCCCC	.	40.0	4.0	34.0	0.0	.	122	.	A|1.000;G|0.000	Atlas-SNP
NUDT22	84304	hgsc.bcm.edu	hg19	11	63994260	63994260	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NUDT22	NM_001128613	exon2	c.G136A	p.E46K	ATCTGGGAGACCC	.	93.0	4.0	78.0	0.0	.	24	.	.	Atlas-SNP
SART1	9092	hgsc.bcm.edu	hg19	11	65745300	65745300	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SART1	NM_005146	exon17	c.A2102G	p.K701R	AGGAGAAGGACGG	.	82.0	4.0	72.0	0.0	.	41	.	.	Atlas-SNP
GSTP1	2950	hgsc.bcm.edu	hg19	11	67352159	67352159	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GSTP1	NM_000852	exon4	c.T148C	p.Y50H	CAGCTATACGGGC	.	116.0	48.0	92.0	0.0	.	21	.	.	Atlas-SNP
CHKA	1119	hgsc.bcm.edu	hg19	11	67821492	67821492	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CHKA	NM_001277	exon12	c.A1337G	p.D446G	TAGGCATCAAACC	.	82.0	4.0	69.0	0.0	.	41	.	.	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	hg19	11	71277087	71277087	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KRTAP5-10	NM_001012710	exon1	c.T454G	p.S152A	TGCTCCTCAGGCT	.	145.0	51.0	157.0	0.0	.	37	.	.	Atlas-SNP
ARHGEF17	9828	hgsc.bcm.edu	hg19	11	73020389	73020389	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ARHGEF17	NM_014786	exon1	c.A706T	p.I236F	TCCTCCATCGCCG	.	226.0	14.0	160.0	0.0	.	117	.	.	Atlas-SNP
C2CD3	26005	hgsc.bcm.edu	hg19	11	73785299	73785299	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	C2CD3	NM_015531	exon24	c.A4950G	p.K1650K	CATACCTTTCAAG	.	100.0	4.0	89.0	0.0	.	288	.	.	Atlas-SNP
C11orf30	56946	hgsc.bcm.edu	hg19	11	76227256	76227256	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	C11orf30	NM_020193	exon11	c.T1584C	p.A528A	TGGAGCTGCAACC	.	95.0	4.0	68.0	0.0	.	123	.	.	Atlas-SNP
PAK1	5058	hgsc.bcm.edu	hg19	11	77090324	77090324	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PAK1	NM_001128620	exon4	c.A401G	p.K134R	GTCTTCTTCGAGT	.	112.0	5.0	59.0	0.0	.	89	.	.	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	hg19	11	82872485	82872485	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PCF11	NM_015885	exon2	c.G309A	p.V103V	TTGTGTGTTTGAA	.	87.0	5.0	66.0	0.0	.	220	.	.	Atlas-SNP
TMEM126A	84233	hgsc.bcm.edu	hg19	11	85365266	85365266	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TMEM126A	NM_032273	exon3	c.T246C	p.T82T	CTTAACTTACAGA	.	61.0	4.0	64.0	0.0	.	20	.	.	Atlas-SNP
CCDC83	220047	hgsc.bcm.edu	hg19	11	85627242	85627242	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC83	NM_173556	exon11	c.A1139G	p.K380R	ATATGAAGTACTT	.	62.0	4.0	91.0	0.0	.	48	.	.	Atlas-SNP
PIWIL4	143689	hgsc.bcm.edu	hg19	11	94335097	94335097	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PIWIL4	NM_152431	exon12	c.T1517C	p.L506S	ACTGCTTGAGAAG	.	74.0	4.0	131.0	0.0	.	70	.	.	Atlas-SNP
GRIA4	2893	hgsc.bcm.edu	hg19	11	105774565	105774565	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GRIA4	NM_001077244	exon8	c.G911A	p.G304E	ATGATGGAGTCCT	.	99.0	4.0	104.0	0.0	.	380	.	.	Atlas-SNP
ZBTB16	7704	hgsc.bcm.edu	hg19	11	114112895	114112895	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZBTB16	NM_006006	exon5	c.A1460G	p.D487G	GCACTGACATGGC	.	54.0	4.0	61.0	0.0	.	101	.	.	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	hg19	11	125474114	125474114	+	Silent	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	STT3A,NS,carcinoma,0,1	STT3A	NM_152713	exon6	c.A480T	p.R160R	CTCCCGATCTGTG	.	92.0	68.0	144.0	1.0	.	52	.	.	Atlas-SNP
ARHGAP32	9743	hgsc.bcm.edu	hg19	11	128932193	128932193	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ARHGAP32	NM_001142685	exon9	c.A903G	p.R301R	CTTGCCTCTCCAC	.	33.0	4.0	42.0	0.0	.	307	.	.	Atlas-SNP
DCP1B	196513	hgsc.bcm.edu	hg19	12	2062353	2062353	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	DCP1B,rectum,carcinoma,0,1	DCP1B	NM_152640	exon7	c.C753G	p.H251Q	CTGCTGGTGGAGA	.	20.0	3.0	13.0	0.0	.	63	.	.	Atlas-SNP
PLEKHG6	55200	hgsc.bcm.edu	hg19	12	6436467	6436467	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLEKHG6	NM_001144856	exon15	c.A1718G	p.D573G	CAGAAGACACAGA	.	85.0	4.0	98.0	0.0	.	62	.	.	Atlas-SNP
CLECL1	160365	hgsc.bcm.edu	hg19	12	9885713	9885713	+	Missense_Mutation	SNP	A	A	T	rs200639830	bycluster	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CLECL1	NM_001267701	exon1	c.T148A	p.Y50N	ATAAGTAAATTGA	.	102.0	6.0	56.0	0.0	.	18	.	.	Atlas-SNP
GUCY2C	2984	hgsc.bcm.edu	hg19	12	14829836	14829836	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GUCY2C	NM_004963	exon7	c.T900C	p.S300S	CCCAGGAGACAGC	.	94.0	4.0	138.0	0.0	.	126	.	.	Atlas-SNP
GUCY2C	2984	hgsc.bcm.edu	hg19	12	14836124	14836124	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	GUCY2C,NS,carcinoma,0,1	GUCY2C	NM_004963	exon4	c.G463A	p.E155K	AGGTTTCTTTATA	.	36.0	2.0	63.0	0.0	.	126	.	.	Atlas-SNP
GUCY2C	2984	hgsc.bcm.edu	hg19	12	14840921	14840921	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GUCY2C	NM_004963	exon2	c.C294A	p.S98R	ACAGGTGCTACTC	.	34.0	25.0	53.0	0.0	.	126	.	.	Atlas-SNP
PLCZ1	89869	hgsc.bcm.edu	hg19	12	18837138	18837138	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PLCZ1,NS,carcinoma,0,1	PLCZ1	NM_033123	exon14	c.T1667G	p.V556G	CCTTCAACAACAA	.	23.0	2.0	32.0	0.0	.	107	.	.	Atlas-SNP
TM7SF3	51768	hgsc.bcm.edu	hg19	12	27128524	27128524	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TM7SF3	NM_016551	exon11	c.C1355T	p.S452F	CTTGTGGACCAGT	.	101.0	73.0	127.0	0.0	.	41	.	.	Atlas-SNP
ARID2	196528	hgsc.bcm.edu	hg19	12	46231166	46231166	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ARID2	NM_152641	exon9	c.T1086C	p.C362C	AAAATGTCTAATG	.	84.0	4.0	73.0	0.0	.	311	.	.	Atlas-SNP
DDX23	9416	hgsc.bcm.edu	hg19	12	49226344	49226344	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DDX23	NM_004818	exon14	c.A1816G	p.T606A	TGGCCGTGAACAT	.	73.0	4.0	53.0	0.0	.	82	.	.	Atlas-SNP
FKBP11	51303	hgsc.bcm.edu	hg19	12	49318403	49318403	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FKBP11	NM_016594	exon3	c.A224G	p.D75G	GAGGTGTCAATAA	.	91.0	4.0	54.0	0.0	.	12	.	.	Atlas-SNP
LMBR1L	55716	hgsc.bcm.edu	hg19	12	49498580	49498580	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LMBR1L	NM_018113	exon4	c.T280C	p.S94P	GCAGGGAGAGCAG	.	100.0	4.0	82.0	0.0	.	61	.	.	Atlas-SNP
BIN2	51411	hgsc.bcm.edu	hg19	12	51693495	51693495	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BIN2	NM_016293	exon6	c.A412G	p.R138G	CAATTCTCTCCTG	.	71.0	4.0	39.0	0.0	.	58	.	.	Atlas-SNP
GRASP	160622	hgsc.bcm.edu	hg19	12	52407934	52407934	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GRASP	NM_181711	exon7	c.A631G	p.K211E	TATGAGAAGTGGG	.	99.0	4.0	74.0	0.0	.	23	.	.	Atlas-SNP
STAT6	6778	hgsc.bcm.edu	hg19	12	57499264	57499264	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	STAT6	NM_001178079	exon8	c.A799G	p.T267A	CGAGGGTTCTCAG	.	77.0	4.0	42.0	0.0	.	69	.	.	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	hg19	12	80714407	80714407	+	Silent	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OTOGL	NM_173591	exon33	c.A3981T	p.T1327T	ATTCACAGATTCT	.	86.0	52.0	68.0	0.0	.	235	.	.	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	hg19	12	80747200	80747200	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OTOGL	NM_173591	exon45	c.T5476C	p.C1826R	ACTTCCTGTTTGA	.	131.0	6.0	89.0	0.0	.	235	.	.	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	hg19	12	93155594	93155594	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLEKHG7	NM_001004330	exon9	c.A767G	p.K256R	AAACTAAGTGCAA	.	77.0	4.0	34.0	0.0	.	38	.	.	Atlas-SNP
SRRM4	84530	hgsc.bcm.edu	hg19	12	119568550	119568550	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SRRM4	NM_194286	exon8	c.A682G	p.T228A	TCCAAGACCCTCT	.	43.0	4.0	16.0	0.0	.	131	.	.	Atlas-SNP
LRRC43	254050	hgsc.bcm.edu	hg19	12	122676094	122676094	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LRRC43	NM_001098519	exon6	c.T1069C	p.S357P	AATGAGTCCGCGG	.	79.0	4.0	27.0	0.0	.	105	.	.	Atlas-SNP
TCTN2	79867	hgsc.bcm.edu	hg19	12	124158356	124158356	+	Silent	SNP	A	A	T	rs111689585	alternate_allele	TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TCTN2	NM_024809	exon4	c.A462T	p.S154S	TGCCTCAGGCAAG	.	216.0	118.0	143.0	0.0	.	50	.	A|0.500;G|0.500	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	hg19	12	125435267	125435267	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DHX37	NM_032656	exon22	c.A2952G	p.E984E	CACGATTTCCTGG	.	95.0	4.0	62.0	0.0	.	114	.	.	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	hg19	12	125451369	125451369	+	Silent	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DHX37	NM_032656	exon12	c.A1560T	p.S520S	GGCCCTTGACTTC	.	168.0	69.0	155.0	0.0	.	114	.	.	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	hg19	12	126138907	126138907	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TMEM132B	NM_052907	exon9	c.T2888C	p.L963P	TTACACTCCCATC	.	86.0	4.0	83.0	0.0	.	207	.	.	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	hg19	13	32912226	32912226	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BRCA2	NM_000059	exon11	c.A3734G	p.E1245G	ATATTGAGAATAT	.	39.0	4.0	39.0	0.0	.	812	.	.	Atlas-SNP
CCDC122	160857	hgsc.bcm.edu	hg19	13	44433973	44433973	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCDC122	NM_144974	exon5	c.A390G	p.A130A	TATTTTTGCATAA	.	49.0	35.0	63.0	0.0	.	21	.	.	Atlas-SNP
RCBTB2	1102	hgsc.bcm.edu	hg19	13	49073817	49073817	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RCBTB2	NM_001268	exon13	c.C1324T	p.R442W	AGGCCCGGTAAAC	.	67.0	5.0	81.0	0.0	.	62	.	.	Atlas-SNP
CYSLTR2	57105	hgsc.bcm.edu	hg19	13	49281801	49281801	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CYSLTR2	NM_020377	exon1	c.T848C	p.L283P	ACAGACTGCATAA	.	71.0	4.0	88.0	0.0	.	55	.	.	Atlas-SNP
CAB39L	81617	hgsc.bcm.edu	hg19	13	49913821	49913821	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CAB39L	NM_030925	exon7	c.T682C	p.S228P	TTAAAGACTGTCT	.	92.0	4.0	126.0	0.0	.	35	.	.	Atlas-SNP
ATP7B	540	hgsc.bcm.edu	hg19	13	52532539	52532539	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	ATP7B,rectum,carcinoma,0,1	ATP7B	NM_000053	exon8	c.A2263G	p.K755E	CCGCCTTCTCAGC	.	88.0	5.0	99.0	0.0	.	123	.	.	Atlas-SNP
VPS36	51028	hgsc.bcm.edu	hg19	13	52992177	52992177	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VPS36	NM_016075	exon11	c.A855G	p.E285E	TAAATCTTCTGGT	.	41.0	4.0	55.0	0.0	.	38	.	.	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	hg19	14	20840992	20840992	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TEP1	NM_007110	exon49	c.A6976G	p.I2326V	ACCAGATCAGAGC	.	98.0	5.0	69.0	0.0	.	224	.	.	Atlas-SNP
NDRG2	57447	hgsc.bcm.edu	hg19	14	21488710	21488710	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NDRG2	NM_201537	exon8	c.T500C	p.V167A	ATGAGGACAAGAC	.	84.0	4.0	66.0	0.0	.	37	.	.	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	hg19	14	23532238	23532238	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ACIN1	NM_014977	exon14	c.A2957G	p.K986R	CCGGACTTCTGCT	.	82.0	4.0	71.0	0.0	.	147	.	.	Atlas-SNP
CTSG	1511	hgsc.bcm.edu	hg19	14	25044539	25044539	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CTSG	NM_001911	exon2	c.T135C	p.G45G	GCTCTGACCTGCT	.	82.0	4.0	68.0	0.0	.	63	.	.	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	hg19	14	35272095	35272095	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	BAZ1A	NM_182648	exon7	c.A826G	p.R276G	TCCCTCTTCGTCT	.	68.0	4.0	39.0	0.0	.	128	.	.	Atlas-SNP
PPP2R3C	55012	hgsc.bcm.edu	hg19	14	35585916	35585916	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	PPP2R3C,right_upper_lobe,carcinoma,0,1	PPP2R3C	NM_017917	exon2	c.A86G	p.D29G	TCTTCATCTTTTA	.	55.0	4.0	39.0	0.0	.	44	.	.	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	hg19	14	36128344	36128344	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	RALGAPA1_ENST00000307138,bladder,carcinoma,0,2	RALGAPA1	NM_194301	exon27	c.G3869A	p.R1290Q	ACCTACCGTGCAG	.	28.0	2.0	27.0	1.0	.	289	.	.	Atlas-SNP
CLEC14A	161198	hgsc.bcm.edu	hg19	14	38725216	38725216	+	Silent	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CLEC14A	NM_175060	exon1	c.G12T	p.A4A	GGCGAACGCCGGC	.	85.0	46.0	38.0	0.0	.	83	.	.	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	hg19	14	45623916	45623916	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FANCM	NM_020937	exon7	c.A1200G	p.K400K	GTCAAAAAATGAA	.	75.0	23.0	68.0	0.0	.	225	.	.	Atlas-SNP
WDHD1	11169	hgsc.bcm.edu	hg19	14	55408356	55408356	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WDHD1	NM_007086	exon26	c.A3242G	p.K1081R	CGCTTCTTTGCTT	.	82.0	4.0	138.0	0.0	.	82	.	.	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	hg19	14	65249105	65249105	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPTB	NM_001024858	exon19	c.A4169G	p.D1390G	TTGAGGTCAGCAT	.	94.0	4.0	100.0	0.0	.	378	.	.	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	hg19	14	75070369	75070369	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LTBP2	NM_000428	exon2	c.A534G	p.T178T	TGCTGTTGTCCAT	.	94.0	4.0	165.0	0.0	.	158	.	.	Atlas-SNP
YLPM1	56252	hgsc.bcm.edu	hg19	14	75230847	75230847	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	YLPM1	NM_019589	exon1	c.A655G	p.S219G	TATTTGAGCCATT	.	91.0	4.0	129.0	0.0	.	298	.	.	Atlas-SNP
C14orf166B	145497	hgsc.bcm.edu	hg19	14	77292857	77292857	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	C14orf166B	NM_194287	exon1	c.T19C	p.S7P	TTCCCATCAAAGC	.	73.0	5.0	83.0	0.0	.	52	.	.	Atlas-SNP
WDR20	91833	hgsc.bcm.edu	hg19	14	102676047	102676047	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WDR20	NM_001242417	exon4	c.T1633C	p.C545R	CCCCTGTGTCCTC	.	61.0	4.0	103.0	0.0	.	35	.	.	Atlas-SNP
TRPM1	4308	hgsc.bcm.edu	hg19	15	31355371	31355371	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TRPM1	NM_001252020	exon7	c.A966G	p.G322G	GGCACGTCCGCTG	.	94.0	36.0	61.0	0.0	.	183	.	.	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	hg19	15	33993260	33993260	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RYR3	NM_001243996	exon42	c.A6462G	p.L2154L	GAGCTTAGAGGAA	.	72.0	4.0	60.0	0.0	.	760	.	.	Atlas-SNP
AQR	9716	hgsc.bcm.edu	hg19	15	35222481	35222481	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	AQR	NM_014691	exon12	c.A992T	p.Y331F	CTATCATAGTGAA	.	35.0	11.0	27.0	0.0	.	139	.	.	Atlas-SNP
PLCB2	5330	hgsc.bcm.edu	hg19	15	40584596	40584596	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLCB2	NM_004573	exon22	c.T2375C	p.M792T	GCAGGCATGGTGA	.	80.0	4.0	64.0	0.0	.	177	.	.	Atlas-SNP
MGA	23269	hgsc.bcm.edu	hg19	15	42003112	42003112	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MGA	NM_001080541	exon8	c.T2649C	p.S883S	TACCTCTTATTCT	.	65.0	4.0	61.0	0.0	.	264	.	.	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	hg19	15	42173320	42173320	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SPTBN5	NM_016642	exon13	c.A2465G	p.E822G	TCAGGCTCAGCTG	.	100.0	4.0	98.0	0.0	.	171	.	.	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	hg19	15	52350974	52350974	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MAPK6	NM_002748	exon4	c.T845C	p.L282P	AGCTGCTTCCAGG	.	94.0	4.0	76.0	0.0	.	70	.	.	Atlas-SNP
DAPK2	23604	hgsc.bcm.edu	hg19	15	64275877	64275877	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DAPK2	NM_014326	exon3	c.C169T	p.R57W	TCTGCCGCTTCTT	.	108.0	20.0	39.0	0.0	.	31	.	.	Atlas-SNP
DPP8	54878	hgsc.bcm.edu	hg19	15	65739300	65739300	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DPP8	NM_197960	exon21	c.A2619G	p.G873G	ATGTTCTCCCGAT	.	112.0	5.0	50.0	0.0	.	78	.	.	Atlas-SNP
ANKRD34C	390616	hgsc.bcm.edu	hg19	15	79587136	79587136	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ANKRD34C	NM_001146341	exon2	c.A1510T	p.R504X	CCAAAGAGAGTTG	.	60.0	36.0	52.0	0.0	.	29	.	.	Atlas-SNP
CPEB1	64506	hgsc.bcm.edu	hg19	15	83296065	83296065	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CPEB1	NM_030594	exon2	c.T69C	p.A23A	GGAGAGAGCAGGT	.	87.0	4.0	57.0	0.0	.	114	.	.	Atlas-SNP
SLC28A1	9154	hgsc.bcm.edu	hg19	15	85438313	85438313	+	Silent	SNP	C	C	T	rs2277576		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	SLC28A1_ENST00000338602,NS,carcinoma,0,1	SLC28A1	NM_201651	exon6	c.C420T	p.L140L	GTTTCTCAAGCCT	.	124.0	5.0	67.0	1.0	.	118	.	.	Atlas-SNP
WDR90	197335	hgsc.bcm.edu	hg19	16	699822	699822	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WDR90	NM_145294	exon2	c.T70C	p.S24P	AAGCGCTCCGCCA	.	37.0	4.0	33.0	0.0	.	107	.	.	Atlas-SNP
CCNF	899	hgsc.bcm.edu	hg19	16	2487180	2487180	+	Missense_Mutation	SNP	C	C	T	rs138913390		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CCNF	NM_001761	exon5	c.C397T	p.R133C	GCCTCTCGCTTCT	.	58.0	4.0	47.0	0.0	.	110	.	C|1.000;T|0.000	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	hg19	16	3254975	3254975	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	OR1F1	NM_012360	exon1	c.T729C	p.S243S	TGGTTCTCACCTG	.	83.0	4.0	158.0	0.0	.	36	.	.	Atlas-SNP
ADCY9	115	hgsc.bcm.edu	hg19	16	4039054	4039054	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ADCY9	NM_001116	exon6	c.A2251G	p.S751G	TCAGGCTGAACTG	.	37.0	4.0	54.0	0.0	.	151	.	.	Atlas-SNP
ERCC4	2072	hgsc.bcm.edu	hg19	16	14024746	14024746	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ERCC4	NM_005236	exon5	c.A972G	p.S324S	GAATTCAGGTGGG	.	54.0	4.0	66.0	0.0	.	100	.	.	Atlas-SNP
USP31	57478	hgsc.bcm.edu	hg19	16	23117594	23117594	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	USP31	NM_020718	exon4	c.A893G	p.Q298R	TTGCTCTGTTTCT	.	113.0	5.0	92.0	0.0	.	122	.	.	Atlas-SNP
ITGAL	3683	hgsc.bcm.edu	hg19	16	30507878	30507878	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ITGAL	NM_002209	exon15	c.T1823C	p.I608T	AGATGATCGTGCT	.	119.0	6.0	81.0	0.0	.	149	.	.	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	hg19	16	31088548	31088548	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZNF646	NM_014699	exon2	c.T903C	p.R301R	CCCCCGTGTCTTC	.	87.0	4.0	58.0	0.0	.	133	.	.	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	hg19	16	66423413	66423413	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CDH5	NM_001795	exon5	c.T769C	p.F257L	TTCCCCTTCTTCA	.	75.0	4.0	84.0	0.0	.	111	.	.	Atlas-SNP
E2F4	1874	hgsc.bcm.edu	hg19	16	67229817	67229817	+	Missense_Mutation	SNP	G	G	A	rs140980388		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	E2F4	NM_001950	exon7	c.G941A	p.S314N	GCAGCAGCAGCAG	.	84.0	15.0	53.0	0.0	.	25	.	.	Atlas-SNP
E2F4	1874	hgsc.bcm.edu	hg19	16	67229823	67229823	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	E2F4	NM_001950	exon7	c.G947A	p.S316N	GCAGCAGCAGCAG	.	89.0	11.0	53.0	0.0	.	25	.	.	Atlas-SNP
KCTD19	146212	hgsc.bcm.edu	hg19	16	67337084	67337084	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KCTD19	NM_001100915	exon4	c.T608C	p.L203P	TCGATGAGGGCCA	.	111.0	5.0	99.0	0.0	.	82	.	.	Atlas-SNP
TSNAXIP1	55815	hgsc.bcm.edu	hg19	16	67861436	67861436	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TSNAXIP1	NM_018430	exon15	c.A1690G	p.K564E	GATGAGAAGGACG	.	85.0	4.0	67.0	0.0	.	66	.	.	Atlas-SNP
EDC4	23644	hgsc.bcm.edu	hg19	16	67916365	67916365	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	EDC4	NM_014329	exon25	c.G3310A	p.D1104N	GCTGCAGACACAT	.	89.0	33.0	70.0	0.0	.	101	.	.	Atlas-SNP
NOB1	28987	hgsc.bcm.edu	hg19	16	69783156	69783156	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NOB1	NM_014062	exon5	c.A485G	p.N162S	AAAGGGTTTCTCC	.	71.0	4.0	51.0	0.0	.	24	.	.	Atlas-SNP
SF3B3	23450	hgsc.bcm.edu	hg19	16	70588379	70588379	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SF3B3	NM_012426	exon12	c.T1433C	p.F478S	TGTCTTTCGTGAA	.	85.0	4.0	73.0	0.0	.	99	.	.	Atlas-SNP
IL34	146433	hgsc.bcm.edu	hg19	16	70688456	70688456	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	IL34	NM_152456	exon3	c.T44A	p.L15H	TCTTCCTTGGCGT	.	190.0	68.0	165.0	0.0	.	26	.	.	Atlas-SNP
FA2H	79152	hgsc.bcm.edu	hg19	16	74761274	74761274	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FA2H	NM_024306	exon3	c.A374G	p.D125G	CGCCAGTCCACCA	.	53.0	4.0	41.0	0.0	.	21	.	.	Atlas-SNP
VPS53	55275	hgsc.bcm.edu	hg19	17	465918	465918	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VPS53	NM_001128159	exon14	c.A1381G	p.T461A	CATCAGTGTTGGG	.	80.0	4.0	81.0	0.0	.	109	.	.	Atlas-SNP
FLII	2314	hgsc.bcm.edu	hg19	17	18148691	18148691	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	FLII	NM_002018	exon29	c.A3652G	p.K1218E	TCAGCTTGATCTC	.	120.0	5.0	51.0	0.0	.	79	.	.	Atlas-SNP
KIAA0100	9703	hgsc.bcm.edu	hg19	17	26961916	26961916	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	KIAA0100	NM_014680	exon16	c.A2689G	p.M897V	CCTTCATCAGCTC	.	74.0	5.0	50.0	0.0	.	175	.	.	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	hg19	17	33807038	33807038	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLFN12L	NM_001195790	exon2	c.G191T	p.R64L	ACAGCTCGTGAGA	.	163.0	71.0	144.0	0.0	.	140	.	.	Atlas-SNP
ACACA	31	hgsc.bcm.edu	hg19	17	35766386	35766386	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ACACA	NM_198834	exon1	c.T4C	p.W2R	ACCACCACATCCT	.	85.0	4.0	85.0	0.0	.	395	.	.	Atlas-SNP
GHDC	84514	hgsc.bcm.edu	hg19	17	40342899	40342899	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GHDC	NM_001142623	exon7	c.C1105T	p.R369X	CCACTCGCACCAC	.	55.0	25.0	59.0	0.0	.	63	.	.	Atlas-SNP
STAT3	6774	hgsc.bcm.edu	hg19	17	40500452	40500452	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	STAT3	NM_003150	exon2	c.T83A	p.M28K	AGCTCCATTGGGA	.	110.0	50.0	106.0	0.0	.	268	.	.	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	hg19	17	56056598	56056598	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VEZF1	NM_007146	exon5	c.A1053G	p.Q351Q	TTGTTGTTGTTGT	.	142.0	10.0	123.0	0.0	.	50	.	.	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	hg19	17	56056601	56056601	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VEZF1	NM_007146	exon5	c.A1050G	p.Q350Q	TTGTTGTTGTTGC	.	142.0	13.0	118.0	0.0	.	50	.	.	Atlas-SNP
MPO	4353	hgsc.bcm.edu	hg19	17	56350840	56350840	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MPO	NM_000250	exon9	c.T1556C	p.M519T	GGTTCCATGGGCT	.	61.0	5.0	42.0	0.0	.	114	.	.	Atlas-SNP
MPO	4353	hgsc.bcm.edu	hg19	17	56350841	56350841	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MPO	NM_000250	exon9	c.A1555C	p.M519L	GTTCCATGGGCTG	.	62.0	6.0	43.0	0.0	.	114	.	.	Atlas-SNP
PRR11	55771	hgsc.bcm.edu	hg19	17	57247212	57247212	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PRR11	NM_018304	exon2	c.A99G	p.T33T	AATTACACCTCCT	.	129.0	6.0	122.0	0.0	.	36	.	.	Atlas-SNP
INTS2	57508	hgsc.bcm.edu	hg19	17	59984985	59984985	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	INTS2	NM_020748	exon8	c.A989G	p.E330G	CTGGTCTCTCTTT	.	121.0	5.0	96.0	0.0	.	89	.	.	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	hg19	17	66879991	66879991	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ABCA8	NM_007168	exon27	c.T3528C	p.T1176T	TCGAAGAGTAAAA	.	111.0	5.0	104.0	0.0	.	213	.	.	Atlas-SNP
SOX9	6662	hgsc.bcm.edu	hg19	17	70120374	70120374	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SOX9	NM_000346	exon3	c.G1376T	p.G459V	GCCAGGGCACCGG	.	77.0	33.0	67.0	0.0	.	91	.	.	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	hg19	18	2738452	2738452	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SMCHD1	NM_015295	exon26	c.G3334A	p.V1112M	CCTGATGTGCAAG	.	82.0	4.0	88.0	0.0	.	88	.	.	Atlas-SNP
ANKRD12	23253	hgsc.bcm.edu	hg19	18	9255794	9255794	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ANKRD12	NM_015208	exon9	c.A2529G	p.K843K	TGAAAAAGAAAAG	.	86.0	4.0	66.0	0.0	.	167	.	.	Atlas-SNP
PSMG2	56984	hgsc.bcm.edu	hg19	18	12718587	12718587	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PSMG2	NM_020232	exon4	c.T360C	p.V120V	CATTGTTCTTTCA	.	84.0	4.0	75.0	0.0	.	17	.	.	Atlas-SNP
RIOK3	8780	hgsc.bcm.edu	hg19	18	21061218	21061218	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RIOK3	NM_003831	exon13	c.A1535G	p.D512G	ATGGAGACCCACC	.	65.0	4.0	49.0	0.0	.	42	.	.	Atlas-SNP
NEDD4L	23327	hgsc.bcm.edu	hg19	18	56008984	56008984	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NEDD4L	NM_001144967	exon15	c.T1332C	p.P444P	CCGGCCTCGTAGC	.	90.0	4.0	84.0	0.0	.	126	.	.	Atlas-SNP
PHLPP1	23239	hgsc.bcm.edu	hg19	18	60563017	60563017	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PHLPP1	NM_194449	exon6	c.A2217G	p.L739L	TAGCTTACAGACA	.	56.0	4.0	63.0	0.0	.	164	.	.	Atlas-SNP
SERPINB12	89777	hgsc.bcm.edu	hg19	18	61232745	61232745	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SERPINB12	NM_080474	exon6	c.T713C	p.V238A	AGGAGGTGAAGGC	.	62.0	6.0	53.0	0.0	.	55	.	.	Atlas-SNP
DOT1L	84444	hgsc.bcm.edu	hg19	19	2216382	2216382	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	DOT1L	NM_032482	exon20	c.A2026G	p.K676E	CGTGGGAAGGGCG	.	106.0	5.0	70.0	0.0	.	205	.	.	Atlas-SNP
MPND	84954	hgsc.bcm.edu	hg19	19	4345914	4345914	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MPND	NM_032868	exon3	c.A467G	p.D156G	AACTGGACAAGTA	.	116.0	5.0	89.0	0.0	.	28	.	.	Atlas-SNP
TICAM1	148022	hgsc.bcm.edu	hg19	19	4817286	4817286	+	Silent	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TICAM1	NM_182919	exon2	c.A1104T	p.S368S	AGTAGATGAAGGA	.	193.0	10.0	166.0	0.0	.	69	.	.	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	hg19	19	5737210	5737210	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_152784	exon6	c.T453C	p.F151F	TTTGTTTTGTGTG	.	60.0	4.0	77.0	0.0	.	.	.	.	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	hg19	19	10112330	10112330	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	COL5A3	NM_015719	exon8	c.A980G	p.D327G	CCACTGTCAGGGT	.	99.0	39.0	71.0	0.0	.	243	.	.	Atlas-SNP
ZNF709	163051	hgsc.bcm.edu	hg19	19	12575010	12575010	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZNF709	NM_152601	exon4	c.C1726T	p.R576X	GCATTCGAACAGA	.	72.0	4.0	57.0	0.0	.	80	.	.	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	hg19	19	15302655	15302655	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NOTCH3	NM_000435	exon5	c.G703A	p.V235M	CGTTCACTTCACA	.	99.0	4.0	95.0	0.0	.	340	.	.	Atlas-SNP
MED26	9441	hgsc.bcm.edu	hg19	19	16687921	16687921	+	Silent	SNP	T	T	C	rs372755647		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MED26	NM_004831	exon3	c.A720G	p.G240G	GCAGGGTCCAGGG	.	99.0	4.0	66.0	0.0	.	25	.	.	Atlas-SNP
PDE4C	5143	hgsc.bcm.edu	hg19	19	18333125	18333125	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PDE4C	NM_000923	exon3	c.T251C	p.L84P	TTTTCCAGGTCAA	.	66.0	4.0	38.0	0.0	.	80	.	.	Atlas-SNP
MAU2	23383	hgsc.bcm.edu	hg19	19	19466193	19466193	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MAU2	NM_015329	exon18	c.T1760C	p.L587P	ACAACCTCATCAC	.	57.0	4.0	33.0	0.0	.	38	.	.	Atlas-SNP
ZNF566	84924	hgsc.bcm.edu	hg19	19	36940828	36940828	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZNF566	NM_001145343	exon5	c.A311G	p.E104G	ATTATTTCCCACT	.	95.0	4.0	120.0	0.0	.	40	.	.	Atlas-SNP
ZNF573	126231	hgsc.bcm.edu	hg19	19	38229627	38229627	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	ZNF573,NS,carcinoma,0,1	ZNF573	NM_001172690	exon5	c.A1764G	p.G588G	GGCCTTTCCACAT	.	49.0	2.0	61.0	0.0	.	63	.	.	Atlas-SNP
PAPL	0	hgsc.bcm.edu	hg19	19	39591791	39591791	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_001004318	exon9	c.T917C	p.V306A	CCCAGGTCCGCAA	.	26.0	4.0	20.0	0.0	.	.	.	.	Atlas-SNP
PSMC4	5704	hgsc.bcm.edu	hg19	19	40486011	40486011	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PSMC4	NM_006503	exon8	c.G876A	p.L292L	GGAGCTGCTGAAT	.	259.0	108.0	224.0	0.0	.	48	.	.	Atlas-SNP
LYPD5	284348	hgsc.bcm.edu	hg19	19	44306520	44306520	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	LYPD5_ENST00000377950,colon,carcinoma,0,1	LYPD5	NM_001031749	exon1	c.G13A	p.V5I	TGGGGACCCCCAT	.	92.0	4.0	59.0	0.0	.	22	.	.	Atlas-SNP
HRC	3270	hgsc.bcm.edu	hg19	19	49657916	49657916	+	Silent	SNP	T	T	C	rs7409255		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HRC	NM_002152	exon1	c.A579G	p.E193E	CTCCTCTTCTCCT	.	157.0	12.0	88.0	0.0	.	85	.	.	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	hg19	19	50100971	50100971	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PRR12	NM_020719	exon4	c.A3379T	p.S1127C	GTCTCCAGCTGCC	.	109.0	43.0	58.0	0.0	.	157	.	.	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	hg19	19	52130941	52130941	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SIGLEC5	NM_003830	exon6	c.A1056G	p.R352R	GGAGCATCTGCAG	.	34.0	13.0	29.0	0.0	.	67	.	.	Atlas-SNP
ZNF665	79788	hgsc.bcm.edu	hg19	19	53668046	53668046	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	ZNF665,NS,carcinoma,0,1	ZNF665	NM_024733	exon4	c.G1697A	p.G566D	TTCTCACCAGTGT	.	71.0	3.0	77.0	0.0	.	136	.	.	Atlas-SNP
VN1R2	317701	hgsc.bcm.edu	hg19	19	53762214	53762214	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	VN1R2	NM_173856	exon1	c.T586C	p.S196P	AGGAACTCCAGGT	.	112.0	6.0	66.0	0.0	.	71	.	.	Atlas-SNP
TMEM150B	284417	hgsc.bcm.edu	hg19	19	55832397	55832397	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TMEM150B	NM_001085488	exon3	c.G8T	p.G3V	AGGTAGCCCCACA	.	163.0	78.0	126.0	0.0	.	19	.	.	Atlas-SNP
ZNF446	55663	hgsc.bcm.edu	hg19	19	58991708	58991708	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ZNF446	NM_017908	exon7	c.A968G	p.E323G	GACTGGAGCCGGC	.	58.0	4.0	80.0	0.0	.	22	.	.	Atlas-SNP
TRIM28	10155	hgsc.bcm.edu	hg19	19	59061183	59061183	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TRIM28	NM_005762	exon14	c.G2062T	p.D688Y	GGTGCAGACAGCA	.	39.0	33.0	75.0	0.0	.	46	.	.	Atlas-SNP
NSFL1C	55968	hgsc.bcm.edu	hg19	20	1434946	1434946	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	NSFL1C	NM_016143	exon5	c.T449C	p.F150S	CCTGCAAATGGCT	.	79.0	5.0	56.0	0.0	.	38	.	.	Atlas-SNP
PTPRA	5786	hgsc.bcm.edu	hg19	20	3007357	3007357	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PTPRA	NM_002836	exon22	c.A1639T	p.N547Y	ATCCAGAATGACA	.	107.0	49.0	68.0	0.0	.	75	.	.	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	hg19	20	25300910	25300910	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ABHD12	NM_001042472	exon4	c.A467G	p.D156G	ATCTGGTCTTTGC	.	81.0	4.0	64.0	0.0	.	46	.	.	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	hg19	20	33575459	33575459	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	MYH7B	NM_020884	exon17	c.A1373T	p.K458M	TGACCAAGGGCCA	.	141.0	32.0	70.0	0.0	.	145	.	.	Atlas-SNP
RBM12	10137	hgsc.bcm.edu	hg19	20	34240764	34240764	+	Silent	SNP	A	A	G	rs201125389		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	RBM12,rectum,NS,0,2	RBM12	NM_001198840	exon2	c.T2481C	p.P827P	GGGGCCAGGCCCA	.	83.0	4.0	43.0	0.0	.	93	.	A|0.996;G|0.004	Atlas-SNP
CNBD2	140894	hgsc.bcm.edu	hg19	20	34611572	34611572	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	NM_080834	exon11	c.T1306C	p.L436L	CGACCCTTGATCC	.	95.0	4.0	71.0	0.0	.	.	.	.	Atlas-SNP
WFDC13	164237	hgsc.bcm.edu	hg19	20	44334544	44334544	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	WFDC13	NM_172005	exon3	c.A282G	p.X94W	CAACTGAGGCATA	.	96.0	4.0	58.0	0.0	.	6	.	.	Atlas-SNP
USP25	29761	hgsc.bcm.edu	hg19	21	17163836	17163836	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	USP25,colon,carcinoma,0,1	USP25	NM_013396	exon5	c.C408T	p.S136S	AGCCAGCATAGCA	.	60.0	4.0	62.0	0.0	.	156	.	.	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	hg19	21	30329699	30329699	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LTN1	NM_015565	exon15	c.G2985A	p.P995P	GTCGTTCGGCATT	.	68.0	4.0	64.0	0.0	.	141	.	.	Atlas-SNP
CLIC6	54102	hgsc.bcm.edu	hg19	21	36081737	36081737	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	CLIC6	NM_053277	exon5	c.C1800T	p.Y600Y	TGCCTACAGCACC	.	61.0	4.0	52.0	0.0	.	49	.	.	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	hg19	21	43223051	43223051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PRDM15	NM_022115	exon30	c.G3862A	p.A1288T	CTTCGGCCAAATC	.	58.0	4.0	29.0	0.0	.	110	.	.	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	hg19	21	47783761	47783761	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PCNT	NM_006031	exon14	c.C2521T	p.R841W	TGTGGGCGGGAGC	.	82.0	41.0	74.0	0.0	.	283	.	.	Atlas-SNP
SERPIND1	3053	hgsc.bcm.edu	hg19	22	21138492	21138492	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SERPIND1	NM_000185	exon3	c.A1122G	p.T374T	ACTGACACCCCGG	.	78.0	4.0	57.0	0.0	.	92	.	.	Atlas-SNP
THAP7	80764	hgsc.bcm.edu	hg19	22	21354195	21354195	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	THAP7	NM_030573	exon4	c.A904G	p.M302V	GCTGCATGGCAAA	.	88.0	4.0	67.0	0.0	.	15	.	.	Atlas-SNP
UBE2L3	7332	hgsc.bcm.edu	hg19	22	21922044	21922044	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	UBE2L3	NM_003347	exon1	c.G11T	p.S4I	CGGCCAGCAGGAG	.	153.0	57.0	141.0	0.0	.	11	.	.	Atlas-SNP
PLA2G3	50487	hgsc.bcm.edu	hg19	22	31531911	31531911	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PLA2G3	NM_015715	exon7	c.A1328G	p.D443G	CTAGGGTCTCTGG	.	72.0	4.0	38.0	0.0	.	85	.	.	Atlas-SNP
SEPT3	55964	hgsc.bcm.edu	hg19	22	42392914	42392914	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SEPT3	NM_145733	exon11	c.C1020T	p.G340G	AGAAGGCCTCCTG	.	88.0	4.0	90.0	0.0	.	53	.	.	Atlas-SNP
TCF20	6942	hgsc.bcm.edu	hg19	22	42610352	42610352	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TCF20	NM_181492	exon1	c.A960G	p.Q320Q	TTGTTGTTGCTGC	.	193.0	9.0	128.0	0.0	.	164	.	.	Atlas-SNP
LDOC1L	84247	hgsc.bcm.edu	hg19	22	44892949	44892949	+	Missense_Mutation	SNP	C	C	T	rs374819770		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	LDOC1L	NM_032287	exon2	c.G488A	p.R163H	TTGTTGCGCAAGG	.	98.0	36.0	78.0	0.0	.	24	.	.	Atlas-SNP
TYMP	1890	hgsc.bcm.edu	hg19	22	50967939	50967939	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	TYMP	NM_001257989	exon2	c.A200G	p.Q67R	GCGCCCTGCGCGC	.	96.0	4.0	103.0	0.0	.	25	.	.	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	hg19	X	1522164	1522164	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ASMTL	NM_004192	exon13	c.T1864G	p.X622G	GGCTTCAGGGGGC	.	81.0	8.0	66.0	0.0	.	56	.	.	Atlas-SNP
PRKX	5613	hgsc.bcm.edu	hg19	X	3631158	3631158	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	PRKX	NM_005044	exon1	c.T137C	p.L46P	TCCTGCAGGCTGT	.	74.0	4.0	38.0	0.0	.	29	.	.	Atlas-SNP
RBBP7	5931	hgsc.bcm.edu	hg19	X	16876930	16876930	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RBBP7	NM_001198719	exon4	c.A482G	p.E161G	TTAATTTCACATT	.	91.0	4.0	87.0	0.0	.	58	.	.	Atlas-SNP
YY2	404281	hgsc.bcm.edu	hg19	X	21875262	21875262	+	Silent	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	YY2	NM_206923	exon1	c.T660A	p.P220P	ACTTCCTCCTGGG	.	110.0	46.0	87.0	0.0	.	43	.	.	Atlas-SNP
RLIM	51132	hgsc.bcm.edu	hg19	X	73814206	73814206	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	RLIM	NM_183353	exon4	c.A188T	p.E63V	AGCAACTCTTCCT	.	108.0	34.0	94.0	0.0	.	90	.	.	Atlas-SNP
ATRX	546	hgsc.bcm.edu	hg19	X	76812950	76812950	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ATRX	NM_000489	exon30	c.A6671G	p.K2224R	CTCTTCTTCTTCT	.	98.0	4.0	80.0	0.0	.	833	.	.	Atlas-SNP
ATRX	546	hgsc.bcm.edu	hg19	X	76856034	76856034	+	Splice_Site	SNP	C	C	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	ATRX	NM_000489	exon24	c.5567-1G>A	.	CCACACCTGATCA	.	104.0	47.0	92.0	0.0	.	833	.	.	Atlas-SNP
GPR119	139760	hgsc.bcm.edu	hg19	X	129518585	129518585	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	GPR119	NM_178471	exon1	c.T837C	p.Y279Y	ATAGGCATAGATG	.	95.0	6.0	133.0	0.0	.	34	.	.	Atlas-SNP
ND6	0	hgsc.bcm.edu	hg19	MT	14604	14604	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	.	ENST00000361681	exon1	c.T70A	p.S24T	TAGGAGAAGGCTT	.	18.0	10.0	27.0	0.0	.	.	.	.	Atlas-SNP
SLITRK6	84189	hgsc.bcm.edu	hg19	13	86369191	86369191	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	SLITRK6	NM_032229	exon2	c.1454delC	p.T485fs	.	.	62.0	53.0	60.0	0.0	.	150	.	.	Atlas-Indel,Pindel
INPP5A	3632	hgsc.bcm.edu	hg19	10	134523851	134523851	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	INPP5A	NM_005539	exon8	c.537delC	p.D179fs	.	.	137.0	55.0	99.0	0.0	.	77	.	.	Atlas-Indel,Pindel
HNF4G	3174	hgsc.bcm.edu	hg19	8	76456117	76456118	+	Frame_Shift_Ins	INS	-	-	ACAGAGC	novel		TCGA-BC-A3KF-01A-11D-A20W-10	TCGA-BC-A3KF-10A-01D-A20W-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	5df8ad51-b7d4-46a0-a522-f6c9a38067ff	90e68f39-b72a-45ea-85ff-92e633f5c29c	.	HNF4G	NM_004133	exon2	c.160_161insACAGAGC	p.D54fs	.	.	130.0	12.0	0.0	0.0	.	111	.	.	Pindel
