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
SERINC2	347735	hgsc.bcm.edu	hg19	1	31907019	31907019	+	Silent	SNP	C	C	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	SERINC2	NM_001199038	exon11	c.C1368A	p.L456L	CCCACTCCTCCTG	.	35.0	29.0	54.0	0.0	.	44	.	.	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	hg19	1	79403615	79403615	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ELTD1	NM_022159	exon6	c.T637A	p.L213I	CAGATAACTTGTC	.	371.0	114.0	296.0	0.0	.	143	.	.	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	hg19	1	145532146	145532146	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ITGA10	NM_003637	exon8	c.C790T	p.R264X	GGGGGCCGACCCG	.	62.0	14.0	51.0	0.0	.	131	.	.	Atlas-SNP
TP53BP2	7159	hgsc.bcm.edu	hg19	1	224002032	224002032	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	TP53BP2	NM_001031685	exon3	c.C199T	p.R67X	ACATTCGCTCATT	.	60.0	9.0	30.0	0.0	.	144	.	.	Atlas-SNP
DTNB	1838	hgsc.bcm.edu	hg19	2	25611083	25611083	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	DTNB,colon,carcinoma,0,1	DTNB	NM_021907	exon17	c.G1723A	p.A575T	CGAAGGCCTCCTG	.	22.0	12.0	33.0	1.0	.	43	.	.	Atlas-SNP
TGOLN2	10618	hgsc.bcm.edu	hg19	2	85552051	85552051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	TGOLN2	NM_001206841	exon3	c.G1295A	p.R432H	TCCAAACGTTGGT	.	114.0	35.0	99.0	0.0	.	32	.	.	Atlas-SNP
AMER3	205147	hgsc.bcm.edu	hg19	2	131521437	131521437	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	.	NM_152698	exon2	c.G1792A	p.D598N	TCCAGGGATGCCT	.	47.0	21.0	65.0	0.0	.	.	.	.	Atlas-SNP
CDCA7	83879	hgsc.bcm.edu	hg19	2	174224139	174224139	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	CDCA7,NS,carcinoma,0,2	CDCA7	NM_031942	exon3	c.G304A	p.E102K	ACTAACGAACTGG	.	210.0	64.0	177.0	1.0	.	48	.	.	Atlas-SNP
IL17RD	54756	hgsc.bcm.edu	hg19	3	57154328	57154328	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	IL17RD	NM_017563	exon2	c.C140T	p.A47V	CTGCTGGCTGGCC	.	95.0	31.0	85.0	0.0	.	93	.	.	Atlas-SNP
ACAD11	84129	hgsc.bcm.edu	hg19	3	132349391	132349391	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ACAD11	NM_032169	exon7	c.A853T	p.M285L	CTTCCATTGATGG	.	125.0	22.0	132.0	0.0	.	78	.	.	Atlas-SNP
EHHADH	1962	hgsc.bcm.edu	hg19	3	184911175	184911175	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	EHHADH	NM_001966	exon7	c.C1011A	p.N337K	CATCTTGTTTGCA	.	108.0	33.0	166.0	0.0	.	73	.	.	Atlas-SNP
RTP1	132112	hgsc.bcm.edu	hg19	3	186917604	186917604	+	Missense_Mutation	SNP	C	C	T	rs372732386		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	RTP1	NM_153708	exon2	c.C538T	p.R180C	GCCAGCCGCCAGG	.	32.0	18.0	29.0	0.0	.	51	.	.	Atlas-SNP
IBSP	3381	hgsc.bcm.edu	hg19	4	88732600	88732600	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	IBSP	NM_004967	exon7	c.A492T	p.E164D	CGAAGAAAGCGAA	.	151.0	53.0	197.0	0.0	.	53	.	.	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	hg19	4	187455191	187455191	+	Silent	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	MTNR1A	NM_005958	exon2	c.G705A	p.R235R	AAAATTCCTGAAG	.	192.0	47.0	162.0	0.0	.	46	.	.	Atlas-SNP
DSP	1832	hgsc.bcm.edu	hg19	6	7583427	7583427	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	DSP,NS,carcinoma,0,1	DSP	NM_004415	exon24	c.A5932G	p.M1978V	ACAGCAATGCAGC	.	126.0	56.0	132.0	1.0	.	306	.	.	Atlas-SNP
HIST1H2AG	8969	hgsc.bcm.edu	hg19	6	27101166	27101166	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	HIST1H2AG	NM_021064	exon1	c.G316T	p.G106C	GCACAGGGCGGTG	.	134.0	53.0	186.0	0.0	.	37	.	.	Atlas-SNP
HMGCLL1	54511	hgsc.bcm.edu	hg19	6	55360266	55360266	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	HMGCLL1,NS,carcinoma,0,1	HMGCLL1	NM_019036	exon8	c.G836C	p.C279S	TCATGACAGTGAA	.	160.0	64.0	203.0	0.0	.	70	.	.	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	hg19	6	152651593	152651593	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	SYNE1	NM_182961	exon78	c.A14227C	p.T4743P	GACCTGTGCTGCG	.	49.0	25.0	69.0	0.0	.	3227	.	.	Atlas-SNP
TWISTNB	221830	hgsc.bcm.edu	hg19	7	19738145	19738145	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	TWISTNB	NM_001002926	exon4	c.T811C	p.W271R	CCTCCCAGATGCC	.	158.0	59.0	192.0	0.0	.	63	.	.	Atlas-SNP
AUTS2	26053	hgsc.bcm.edu	hg19	7	70252291	70252291	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	AUTS2	NM_015570	exon18	c.C2405T	p.S802L	CTCCGTCGTTCCC	.	73.0	31.0	81.0	0.0	.	173	.	.	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	hg19	8	113421218	113421218	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	CSMD3	NM_198123	exon33	c.T5439A	p.D1813E	AACAACATCGTGG	.	134.0	58.0	160.0	0.0	.	2325	.	.	Atlas-SNP
RAB18	22931	hgsc.bcm.edu	hg19	10	27826828	27826828	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	RAB18	NM_001256410	exon8	c.G556A	p.G186S	TGTGATGGTGTAC	.	81.0	31.0	96.0	0.0	.	18	.	.	Atlas-SNP
C10orf137	26098	hgsc.bcm.edu	hg19	10	127426555	127426555	+	Silent	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	C10orf137_ENST00000356792,NS,adenocarcinoma,0,4	C10orf137	NM_001202438	exon14	c.A1827G	p.L609L	TGTTCTAGAGGTA	.	246.0	87.0	284.0	0.0	.	153	.	.	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	hg19	12	13716219	13716219	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	GRIN2B	NM_000834	exon13	c.C3953G	p.A1318G	CGCGGGGCCAGGG	.	186.0	93.0	184.0	0.0	.	303	.	.	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	hg19	12	41410483	41410483	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	CNTN1	NM_001843	exon19	c.2185-1G>A	.	TATTTAGCCTTTG	.	125.0	57.0	126.0	0.0	.	207	.	.	Atlas-SNP
RBMS2	5939	hgsc.bcm.edu	hg19	12	56975266	56975266	+	Missense_Mutation	SNP	C	C	T	rs376730098		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	RBMS2	NM_002898	exon7	c.C706T	p.R236W	AATGGACGGGCTT	.	45.0	21.0	39.0	0.0	.	29	.	.	Atlas-SNP
USP15	9958	hgsc.bcm.edu	hg19	12	62775287	62775287	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	USP15	NM_001252078	exon9	c.C932T	p.P311L	ACACACCTCCACT	.	71.0	31.0	79.0	0.0	.	105	.	.	Atlas-SNP
PIWIL1	9271	hgsc.bcm.edu	hg19	12	130834407	130834407	+	Silent	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	PIWIL1	NM_004764	exon9	c.C939T	p.N313N	GTATAACAATAAG	.	66.0	33.0	101.0	0.0	.	157	.	.	Atlas-SNP
GPR12	2835	hgsc.bcm.edu	hg19	13	27332981	27332981	+	Silent	SNP	C	C	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	GPR12	NM_005288	exon2	c.G984A	p.A328A	CGAGCGCGCTCTC	.	86.0	30.0	107.0	0.0	.	67	.	.	Atlas-SNP
HECTD1	25831	hgsc.bcm.edu	hg19	14	31597908	31597908	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	HECTD1	NM_015382	exon25	c.C4669T	p.R1557W	TAGTCCGTGCTAT	.	234.0	97.0	276.0	1.0	.	159	.	.	Atlas-SNP
MYO1E	4643	hgsc.bcm.edu	hg19	15	59450529	59450529	+	Silent	SNP	A	A	C	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	MYO1E	NM_004998	exon25	c.T2835G	p.T945T	ATTTTGAGTCCCA	.	165.0	81.0	209.0	0.0	.	99	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651	bycluster	TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	TP53_ENST00000545858,NS,adenocarcinoma,+1,16	TP53	NM_000546	exon7	c.C742T	p.R248W	GCCTCCGGTTCAT	.	46.0	31.0	114.0	1.0	.	33396	.	.	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	hg19	17	10404040	10404040	+	Silent	SNP	T	T	C	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	MYH1	NM_005963	exon28	c.A3768G	p.L1256L	ATCTTCTAGAGCG	.	108.0	25.0	114.0	0.0	.	403	.	.	Atlas-SNP
MAPT	4137	hgsc.bcm.edu	hg19	17	44051811	44051811	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	MAPT	NM_005910	exon4	c.A281G	p.H94R	AGCCCCACACGGA	.	38.0	19.0	43.0	0.0	.	135	.	.	Atlas-SNP
IGF2BP1	10642	hgsc.bcm.edu	hg19	17	47117454	47117454	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	IGF2BP1	NM_006546	exon7	c.818+1G>A	.	CAAAACGTAAGTC	.	61.0	24.0	85.0	0.0	.	80	.	.	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	hg19	19	22364341	22364341	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ZNF676	NM_001001411	exon3	c.G178C	p.E60Q	AATCTTCTATGCC	.	115.0	54.0	122.0	0.0	.	146	.	.	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	hg19	19	40360958	40360958	+	Silent	SNP	G	G	T	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	FCGBP	NM_003890	exon33	c.C15450A	p.R5150R	AAAACAGCGGGTG	.	47.0	19.0	69.0	0.0	.	416	.	.	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	hg19	19	40360959	40360959	+	Missense_Mutation	SNP	C	C	T	rs371263426	alternate_allele	TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	FCGBP	NM_003890	exon33	c.G15449A	p.R5150H	AAACAGCGGGTGG	.	47.0	18.0	68.0	0.0	.	416	.	.	Atlas-SNP
KLK12	43849	hgsc.bcm.edu	hg19	19	51535232	51535232	+	Silent	SNP	G	G	A	rs371203521		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	KLK12	NM_019598	exon4	c.C357T	p.R119R	GGTTACGCGGACG	.	32.0	15.0	15.0	0.0	.	30	.	.	Atlas-SNP
ASXL1	171023	hgsc.bcm.edu	hg19	20	31023622	31023622	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ASXL1	NM_015338	exon12	c.A3107G	p.N1036S	AACCCAATTGGAA	.	49.0	21.0	53.0	0.0	.	1114	.	.	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	hg19	20	61528282	61528282	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	DIDO1	NM_080797	exon7	c.C1655T	p.P552L	CCTGGAGGGGCTG	.	84.0	29.0	93.0	0.0	.	321	.	.	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	hg19	22	26294307	26294307	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	MYO18B	NM_032608	exon29	c.A4702G	p.K1568E	GGGGCCAAGAAGA	.	78.0	34.0	77.0	0.0	.	322	.	.	Atlas-SNP
ARX	170302	hgsc.bcm.edu	hg19	X	25033826	25033826	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	ARX	NM_139058	exon1	c.G29C	p.C10S	TCGGAGCAGCCCT	.	361.0	83.0	341.0	0.0	.	19	.	.	Atlas-SNP
NXF3	56000	hgsc.bcm.edu	hg19	X	102335094	102335094	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	NXF3	NM_022052	exon11	c.G978T	p.K326N	TAACCTCTTGTGG	.	88.0	37.0	76.0	0.0	.	81	.	.	Atlas-SNP
CYTB	0	hgsc.bcm.edu	hg19	MT	15719	15719	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	.	ENST00000361789	exon1	c.T973C	p.Y325H	TCACTTTATTGAC	.	283.0	254.0	1299.0	2.0	.	.	.	.	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	hg19	3	121158902	121158903	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	POLQ	NM_199420	exon27	c.7326_7327del	p.2442_2443del	.	.	61.0	23.0	64.0	0.0	.	273	.	.	Atlas-Indel,Pindel
TCF7L1	83439	hgsc.bcm.edu	hg19	2	85536399	85536400	+	In_Frame_Ins	INS	-	-	GCA	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	TCF7L1	NM_031283	exon12	c.1581_1582insGCA	p.A527delinsAA	.	.	66.0	19.0	71.0	0.0	.	44	.	.	Atlas-INDEL
HNRNPL	3191	hgsc.bcm.edu	hg19	19	39330868	39330869	+	In_Frame_Ins	INS	-	-	GGG	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	HNRPL,right_upper_lobe,carcinoma,0,6	HNRNPL	NM_001533	exon8	c.1101_1102insCCC	p.P367delinsPP	.	.	64.0	14.0	86.0	0.0	.	67	.	.	Atlas-INDEL
RNASEL	6041	hgsc.bcm.edu	hg19	1	182551358	182551360	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	RNASEL	NM_021133	exon4	c.1601_1603del	p.534_535del	.	.	219.0	15.0	143.0	0.0	.	83	.	.	Atlas-Indel,Pindel
SLC16A7	9194	hgsc.bcm.edu	hg19	12	60169055	60169056	+	Frame_Shift_Ins	INS	-	-	GTCACCTCTTGTGCCCACTGGCACAGGACTA	novel		TCGA-BC-A216-01A-11D-A152-10	TCGA-BC-A216-11A-11D-A152-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c1d9ed06-7498-4c6c-a0de-dbf28e868109	baf0c971-0005-4e18-bfdf-a2d71a3aff12	.	SLC16A7	NM_001270623	exon5	c.979_980insGTCACCTCTTGTGCCCACTGGCACAGGACTA	p.C327_H328delinsCHLLCPLAQDX	.	.	172.0	19.0	238.0	0.0	.	82	.	.	Pindel