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	TranscriptID	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov_SOL	TVarCov_SOL	NTotCov_SOL	NVarCov_SOL	dbSNPPopFreq	COSMIC_Gene_Freq
A2ML1	144568	bcgsc.ca	37	12	8976339	8976339	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	A2ML1	NM_144670	exon3	c.A270G	p.T90T	.	.	69	6	80	0	.	93
ABCA13	154664	bcgsc.ca	37	7	48349562	48349562	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ABCA13	NM_152701	exon24	c.A9340G	p.T3114A	.	.	161	5	207	0	.	521
ABCB9	23457	bcgsc.ca	37	12	123433301	123433301	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ABCB9	NM_019625	exon5	c.T923C	p.L308P	.	.	175	7	219	1	.	90
ABCC9	10060	bcgsc.ca	37	12	21998694	21998694	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ABCC9	NM_005691	exon24	c.A2939G	p.K980R	.	.	177	6	166	0	.	96
ABCD2	225	hgsc.bcm.edu;broad.mit.edu	37	12	40013265	40013266	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ABCD2	NM_005164	exon1	c.153_154insA	p.K51fs	.	.	166	10	163	0	.	95
ACACB	32	hgsc.bcm.edu;ucsc.edu	37	12	109617830	109617830	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACACB	NM_001093	exon10	c.C1756T	p.Q586X	.	.	157	49	152	0	.	98
ACPT	93650	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	51298214	51298214	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACPT	NM_033068	exon10	c.C1158T	p.I386I	.	.	163	18	178	0	.	90
ACTN2	88	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	236891012	236891012	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACTN2	NM_001103	exon6	c.C571A	p.H191N	.	.	163	27	111	0	.	95
ACVR2A	92	bcgsc.ca	37	2	148677857	148677857	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ACVR2A	NM_001616	exon8	c.T1021C	p.F341L	.	.	141	5	127	1	.	831
ADAM15	8751	hgsc.bcm.edu;broad.mit.edu	37	1	155029712	155029713	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADAM15	NM_001261464	exon12	c.1227_1228insA	p.E409fs	.	.	157	10	76	0	.	651
ADCY9	115	bcgsc.ca	37	16	4165199	4165199	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADCY9	NM_001116	exon2	c.T245A	p.L82Q	.	.	89	9	49	0	.	139
ADH1A	124	hgsc.bcm.edu;broad.mit.edu	37	4	100205756	100205757	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADH1A	NM_000667	exon5	c.367_368insG	p.T123fs	.	.	181	12	210	0	.	227
ADH7	131	bcgsc.ca	37	4	100349739	100349739	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADH7	NM_001166504	exon3	c.A229G	p.T77A	.	.	132	6	176	0	.	227
ADORA3	140	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	112042806	112042806	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADORA3	NM_000677	exon2	c.G723A	p.L241L	.	.	212	58	223	0	.	156
ADRA1B	147	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	159398905	159398905	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ADRA1B	NM_000679	exon2	c.G969A	p.L323L	.	.	249	131	238	1	.	522
AFAP1L2	84632	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	116060312	116060312	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AFAP1L2	NM_032550	exon14	c.G1680T	p.P560P	.	.	88	43	126	0	.	136
AGAP6	414189	broad.mit.edu;bcgsc.ca	37	10	51768528	51768529	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AGAP6	NM_001077665	exon8	c.643_644insC	p.S215fs	.	.	455	8	745	0	.	1
AGBL1	123624	bcgsc.ca	37	15	86801205	86801205	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_152336	exon8	c.A774G	p.E258E	.	.	70	4	105	0	.	.
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu	37	9	88247814	88247815	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AGTPBP1	NM_015239	exon14	c.1658_1659insT	p.C553fs	.	.	163	13	199	0	.	158
AGXT2L2	85007	hgsc.bcm.edu;broad.mit.edu	37	5	177642304	177642305	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AGXT2L2	NM_153373	exon9	c.1055_1056insA	p.I352fs	.	.	246	17	215	0	.	91
AHCYL1	10768	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	110561690	110561690	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AHCYL1	NM_006621	exon14	c.G1335C	p.L445F	.	.	154	70	176	0	.	91
AK5	26289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	77763544	77763544	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AK5	NM_174858	exon5	c.A611G	p.Q204R	.	.	155	50	156	0	.	227
AKAP13	11214	bcgsc.ca	37	15	86122442	86122442	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AKAP13	NM_007200	exon7	c.A1143G	p.E381E	.	.	132	6	187	3	.	258
ALMS1	7840	bcgsc.ca	37	2	73799575	73799575	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ALMS1	NM_015120	exon16	c.A10568G	p.E3523G	.	.	152	5	171	0	.	142
ALS2CL	259173	ucsc.edu;bcgsc.ca;mdanderson.org	37	3	46722787	46722787	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ALS2CL	NM_001190707	exon13	c.A1385G	p.H462R	.	.	160	27	270	1	.	155
AMER1	139285	bcgsc.ca	37	X	63409997	63409997	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_152424	exon2	c.A3170G	p.E1057G	.	.	120	6	151	0	.	.
ANAPC4	29945	bcgsc.ca	37	4	25408852	25408852	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANAPC4	NM_013367	exon20	c.T1408C	p.F470L	.	.	205	7	204	0	.	293
ANGPTL3	27329	bcgsc.ca	37	1	63068019	63068019	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANGPTL3	NM_014495	exon5	c.G899G	p.X300X	.	.	117	5	106	0	.	130
ANK2	287	bcgsc.ca	37	4	114278242	114278242	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANK2	NM_001148	exon38	c.A8468G	p.E2823G	.	.	201	7	232	1	.	583
ANK2	287	bcgsc.ca	37	4	114278795	114278795	+	Silent	SNP	A	A	G	rs201207915		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANK2	NM_001148	exon38	c.A9021G	p.Q3007Q	.	.	163	7	213	1	A|0.999;G|0.000	583
ANKHD1	54882	bcgsc.ca	37	5	139838208	139838208	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKHD1	NM_017747	exon8	c.1243-2A>G	.	.	.	182	6	147	0	.	185
ANKRD12	23253	hgsc.bcm.edu;broad.mit.edu	37	18	9255075	9255076	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD12	NM_015208	exon9	c.1810_1811insA	p.E604fs	.	.	198	14	280	0	.	92
ANKRD26	22852	hgsc.bcm.edu;broad.mit.edu	37	10	27324037	27324038	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD26	NM_014915	exon24	c.3342_3343insA	p.K1114fs	.	.	178	13	159	0	.	138
ANKRD26P1	124149	bcgsc.ca	37	16	46587943	46587943	+	RNA	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	8	3	26	0	.	.
ANKRD6	22881	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	90333665	90333665	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKRD6	NM_001242809	exon12	c.T1107G	p.N369K	.	.	175	19	226	0	.	93
ANKZF1	55139	bcgsc.ca	37	2	220096739	220096739	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANKZF1	NM_001042410	exon3	c.A238G	p.T80A	.	.	237	7	263	1	.	92
ANTXR1	84168	broad.mit.edu;bcgsc.ca	37	2	69472525	69472526	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ANTXR1	NM_032208	exon18	c.1603_1604insC	p.S535fs	.	.	87	9	134	0	.	94
AP1B1	162	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	22	29736737	29736737	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AP1B1	NM_001127	exon14	c.G1906C	p.D636H	.	.	97	11	92	0	.	92
AP3B1	8546	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	77412060	77412060	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AP3B1	NM_003664	exon19	c.1969-2A>G	.	.	.	208	22	155	0	.	90
APBB1	322	hgsc.bcm.edu;broad.mit.edu	37	11	6423899	6423900	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APBB1	NM_145689	exon7	c.1161_1162insC	p.P387fs	.	.	185	11	275	0	.	136
APEX1	328	hgsc.bcm.edu;broad.mit.edu	37	14	20925388	20925389	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APEX1	NM_080648	exon5	c.678_679insA	p.N226fs	.	.	169	12	206	0	.	661
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496328	39496328	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APOBEC3H	NM_001166003	exon2	c.C45G	p.N15K	.	.	128	9	126	0	.	91
APOC4	346	bcgsc.ca	37	19	45448524	45448524	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	APOC4	NM_001646	exon3	c.T346C	p.C116R	.	.	77	4	47	0	.	153
AQPEP	0	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	5	115298764	115298764	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_173800	exon1	c.C450G	p.F150L	.	.	71	16	53	0	.	.
ARFGEF2	10564	bcgsc.ca	37	20	47626856	47626856	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARFGEF2	NM_006420	exon27	c.C3672T	p.N1224N	.	.	75	4	65	0	.	358
ARFIP2	23647	bcgsc.ca	37	11	6498444	6498444	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARFIP2	NM_001242854	exon8	c.T1024C	p.F342L	.	.	158	6	229	0	.	90
ARHGAP20	57569	bcgsc.ca	37	11	110462778	110462778	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARHGAP20	NM_020809	exon11	c.T1066C	p.S356P	.	.	186	6	253	1	.	230
ARHGAP32	9743	hgsc.bcm.edu;broad.mit.edu	37	11	128842442	128842443	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARHGAP32	NM_001142685	exon21	c.3917_3918insC	p.L1306fs	.	.	169	11	227	0	.	231
ARHGEF16	27237	bcgsc.ca	37	1	3385445	3385445	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARHGEF16	NM_014448	exon5	c.T806C	p.V269A	.	.	215	8	294	2	.	228
ARHGEF28	64283	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	73153515	73153515	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001080479	exon15	c.C1825A	p.P609T	.	.	340	113	300	0	.	.
ARID2	196528	hgsc.bcm.edu;broad.mit.edu	37	12	46246025	46246026	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARID2	NM_152641	exon15	c.4119_4120insA	p.S1373fs	.	.	198	12	165	0	.	100
ARMC9	80210	ucsc.edu;bcgsc.ca;mdanderson.org	37	2	232135735	232135735	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ARMC9	NM_025139	exon13	c.T1160G	p.V387G	.	.	290	112	329	2	.	91
ASNA1	439	bcgsc.ca	37	19	12856547	12856547	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ASNA1	NM_004317	exon4	c.A583G	p.N195D	.	.	46	4	37	0	.	92
ASPM	259266	hgsc.bcm.edu	37	1	197091175	197091176	+	Splice_Site	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ASPM	NM_018136	exon17	c.3742-2->T	.	.	.	245	16	158	0	.	615
ATF7IP	55729	bcgsc.ca	37	12	14634096	14634096	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATF7IP	NM_018179	exon13	c.T3257C	p.V1086A	.	.	62	4	40	0	.	252
ATG14	22863	hgsc.bcm.edu;broad.mit.edu	37	14	55844624	55844625	+	Splice_Site	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATG14	NM_014924	exon10	c.1087-2->T	.	.	.	197	13	202	0	.	90
ATP10B	23120	bcgsc.ca	37	5	160033818	160033818	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATP10B	NM_025153	exon19	c.A3114G	p.I1038M	.	.	249	8	272	0	.	72
ATP6V1D	51382	hgsc.bcm.edu;broad.mit.edu	37	14	67819690	67819691	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATP6V1D	NM_015994	exon2	c.109_110insA	p.S37fs	.	.	184	11	202	0	.	659
ATRNL1	26033	bcgsc.ca	37	10	117228705	117228705	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATRNL1	NM_207303	exon24	c.A3520G	p.T1174A	.	.	124	5	125	0	.	96
ATXN3	4287	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	92548653	92548653	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ATXN3	NM_004993	exon8	c.A766C	p.S256R	.	.	149	27	169	0	.	522
AUTS2	26053	hgsc.bcm.edu;bcgsc.ca	37	7	70255627	70255627	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AUTS2	NM_015570	exon19	c.3425delA	p.E1142fs	.	.	58	13	66	0	.	92
AXDND1	126859	hgsc.bcm.edu;broad.mit.edu	37	1	179437688	179437689	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	AXDND1	NM_144696	exon17	c.1909_1910insA	p.E637fs	.	.	221	15	149	0	.	93
B4GALT3	8703	hgsc.bcm.edu;broad.mit.edu	37	1	161143503	161143504	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	B4GALT3	NM_001199873	exon6	c.695_696insC	p.Q232fs	.	.	147	11	130	0	.	90
BAAT	570	bcgsc.ca	37	9	104133570	104133570	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BAAT	NM_001127610	exon2	c.A117G	p.E39E	.	.	81	4	96	0	.	228
BCLAF1	9774	bcgsc.ca	37	6	136599627	136599627	+	Missense_Mutation	SNP	C	C	T	rs149799182		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BCLAF1	NM_014739	exon4	c.G392A	p.R131Q	.	.	248	79	201	2	C|1.000;T|0.000	228
BICD1	636	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	32490708	32490708	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BICD1	NM_001714	exon7	c.A2528T	p.Q843L	.	.	105	16	98	0	.	153
BMPR2	659	hgsc.bcm.edu	37	2	203420129	203420130	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BMPR2	NM_001204	exon12	c.1741_1742insA	p.E581fs	.	.	184	12	178	0	.	1003
BPNT1	10380	ucsc.edu	37	1	220231338	220231338	+	RNA	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BPNT1	.	.	.	.	.	.	70	1	41	0	.	91
BRCA1	672	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	41223109	41223109	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BRCA1	NM_007300	exon16	c.G4885A	p.A1629T	.	.	262	40	195	0	.	3415
BRD2	6046	hgsc.bcm.edu;ucsc.edu	37	6	32948467	32948467	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BRD2	NM_001199455	exon13	c.C2483A	p.S828X	.	.	93	27	136	0	.	398
BZRAP1	9256	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	56389687	56389687	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	BZRAP1	NM_004758	exon17	c.G2495A	p.R832Q	.	.	85	15	92	0	.	229
C10orf118	55088	bcgsc.ca	37	10	115917391	115917391	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C10orf118	NM_018017	exon3	c.T681C	p.C227C	.	.	212	6	215	0	.	92
C10orf2	56652	bcgsc.ca	37	10	102753199	102753199	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C10orf2	NM_021830	exon5	c.A1987G	p.N663D	.	.	80	5	78	0	.	69
C11orf57	55216	hgsc.bcm.edu;broad.mit.edu	37	11	111953315	111953316	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C11orf57	NM_001082969	exon6	c.501_502insA	p.H167fs	.	.	242	15	305	0	.	155
C11orf63	79864	bcgsc.ca	37	11	122830120	122830120	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C11orf63	NM_024806	exon9	c.T2304C	p.A768A	.	.	125	6	120	0	.	93
C11orf86	254439	hgsc.bcm.edu;broad.mit.edu	37	11	66742903	66742904	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C11orf86	NM_001136485	exon1	c.70_71insG	p.W24fs	.	.	178	11	125	0	.	68
C14orf166B	145497	bcgsc.ca	37	14	77319585	77319585	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_194287	exon9	c.T840C	p.D280D	.	.	213	8	252	0	.	.
C15orf39	56905	bcgsc.ca	37	15	75499878	75499878	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C15orf39	NM_015492	exon2	c.T1489C	p.S497P	.	.	77	5	71	0	.	90
C2orf42	54980	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	70408519	70408519	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C2orf42	NM_017880	exon3	c.G599A	p.S200N	.	.	123	19	150	0	.	90
C4BPA	722	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	207318042	207318042	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C4BPA	NM_000715	exon12	c.A1774T	p.T592S	.	.	150	15	84	0	.	154
C6orf141	135398	broad.mit.edu;bcgsc.ca	37	6	49519124	49519125	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145652	exon1	c.619_620insG	p.W207fs	.	.	55	7	78	0	.	.
C6orf222	389384	bcgsc.ca	37	6	36291924	36291924	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C6orf222	NM_001010903	exon7	c.A1212G	p.E404E	.	.	143	5	186	0	.	93
C6orf62	81688	hgsc.bcm.edu	37	6	24706479	24706480	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	C6orf62	NM_030939	exon5	c.576_577insA	p.N192fs	.	.	179	11	129	0	.	90
C7orf65	401335	bcgsc.ca	37	7	47698611	47698611	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001123065	exon3	c.A241G	p.I81V	.	.	222	8	234	2	.	.
CACNA1A	773	bcgsc.ca	37	19	13346492	13346492	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CACNA1A	NM_001127221	exon32	c.T5006C	p.I1669T	.	.	148	5	158	1	.	67
CAND2	23066	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	12854821	12854821	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CAND2	NM_001162499	exon7	c.T940G	p.Y314D	.	.	171	62	250	0	.	72
CAPN3	825	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	15	42703132	42703132	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CAPN3	NM_000070	exon22	c.G2314A	p.D772N	.	.	204	51	240	0	.	514
CASP8AP2	9994	hgsc.bcm.edu;broad.mit.edu	37	6	90577003	90577004	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CASP8AP2	NM_012115	exon8	c.3994_3995insA	p.E1332fs	.	.	168	10	145	0	.	24
CBX4	8535	hgsc.bcm.edu;broad.mit.edu	37	17	77808830	77808831	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CBX4	NM_003655	exon5	c.611_612insG	p.A204fs	.	.	206	12	78	0	.	228
CCDC141	285025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	179702272	179702272	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCDC141	NM_173648	exon23	c.C3674T	p.S1225F	.	.	103	14	111	0	.	78
CCDC144A	9720	broad.mit.edu;bcgsc.ca	37	17	16614996	16614997	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_014695	exon6	c.1582_1583insA	p.E528fs	.	.	1498	17	2103	0	.	.
CCDC144A	9720	broad.mit.edu;bcgsc.ca	37	17	16615087	16615088	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_014695	exon6	c.1673_1674insA	p.L558fs	.	.	1817	27	2581	0	.	.
CCDC144A	9720	broad.mit.edu;bcgsc.ca	37	17	16638261	16638262	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_014695	exon12	c.2676_2677insA	p.N892fs	.	.	385	12	574	0	.	.
CCDC146	57639	broad.mit.edu;bcgsc.ca	37	7	76889333	76889334	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCDC146	NM_020879	exon8	c.766_767insA	p.E256fs	.	.	91	9	123	0	.	70
CCDC168	643677	hgsc.bcm.edu	37	13	103393521	103393522	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001146197	exon4	c.9526_9527insA	p.L3176fs	.	.	127	12	120	0	.	.
CCDC168	643677	hgsc.bcm.edu;broad.mit.edu	37	13	103396690	103396691	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001146197	exon4	c.6357_6358insA	p.N2119fs	.	.	155	10	177	0	.	.
CCDC168	643677	hgsc.bcm.edu;broad.mit.edu	37	13	103397069	103397070	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001146197	exon4	c.5978_5979insA	p.M1993fs	.	.	188	15	220	0	.	.
CCDC37	348807	hgsc.bcm.edu	37	3	126142435	126142435	+	Missense_Mutation	SNP	G	G	A	rs200815085		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCDC37	NM_182628	exon13	c.G1234A	p.E412K	.	.	71	8	129	0	.	92
CCR2	729230	ucsc.edu;bcgsc.ca	37	3	46399449	46399449	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCR2	NM_001123041	exon2	c.A431G	p.H144R	.	.	387	75	501	1	.	568
CCZ1	51622	broad.mit.edu;bcgsc.ca	37	7	5940158	5940159	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CCZ1	NM_015622	exon3	c.273_274insT	p.Q91fs	.	.	903	11	914	0	.	44
CDC37L1	55664	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	4706065	4706065	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDC37L1	NM_017913	exon7	c.G967A	p.V323M	.	.	269	58	291	0	.	90
CDH20	28316	bcgsc.ca	37	18	59157788	59157788	+	Missense_Mutation	SNP	T	T	C	rs186858310		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDH20	NM_031891	exon1	c.T2C	p.M1T	.	.	209	6	282	0	T|0.999;C|0.000	155
CDK12	51755	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	37627327	37627327	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDK12	NM_016507	exon2	c.G1242C	p.K414N	.	.	174	26	119	0	.	1055
CDK12	51755	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	37687306	37687306	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CDK12	NM_016507	exon14	c.C4210T	p.R1404C	.	.	112	13	138	0	.	1055
CELSR1	9620	hgsc.bcm.edu;broad.mit.edu	37	22	46930690	46930691	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CELSR1	NM_014246	exon1	c.2378_2379insC	p.H793fs	.	.	167	10	139	0	.	525
CEP85L	387119	hgsc.bcm.edu;broad.mit.edu	37	6	118886846	118886847	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001178035	exon4	c.875_876insT	p.P292fs	.	.	300	27	287	0	.	.
CFTR	1080	broad.mit.edu;bcgsc.ca	37	7	117232304	117232305	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CFTR	NM_000492	exon14	c.2083_2084insA	p.E695fs	.	.	79	9	67	0	.	518
CHUK	1147	bcgsc.ca	37	10	101954187	101954187	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CHUK	NM_001278	exon17	c.T1821C	p.H607H	.	.	144	6	140	0	.	961
CLASP2	23122	ucsc.edu;bcgsc.ca	37	3	33626378	33626378	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CLASP2	NM_015097	exon22	c.G2106C	p.L702L	.	.	194	47	204	1	.	93
CLEC14A	161198	bcgsc.ca	37	14	38724406	38724406	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CLEC14A	NM_175060	exon1	c.T822C	p.A274A	.	.	62	5	79	0	.	94
CLECL1	160365	hgsc.bcm.edu	37	12	9885713	9885713	+	Missense_Mutation	SNP	A	A	T	rs200639830		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CLECL1	NM_001267701	exon1	c.T148A	p.Y50N	.	.	144	6	145	0	.	90
CLRN1	7401	bcgsc.ca	37	3	150659378	150659378	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CLRN1	NM_174878	exon2	c.T424C	p.F142L	.	.	213	6	227	0	.	90
CMIP	80790	bcgsc.ca	37	16	81641215	81641215	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_198390	exon2	c.A344G	p.E115G	.	.	71	4	69	0	.	.
CMIP	80790	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	81736275	81736275	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_198390	exon17	c.1944+1G>A	.	.	.	722	368	934	2	.	.
CMTM1	113540	hgsc.bcm.edu;broad.mit.edu	37	16	66600574	66600575	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CMTM1	NM_181268	exon1	c.158_159insC	p.H53fs	.	.	139	10	209	0	.	90
CNEP1R1	255919	bcgsc.ca	37	16	50068059	50068059	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_153261	exon6	c.T379C	p.C127R	.	.	76	4	202	0	.	.
CNKSR1	10256	bcgsc.ca	37	1	26510575	26510575	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CNKSR1	NM_006314	exon10	c.T869C	p.V290A	.	.	143	6	235	3	.	846
CNTLN	54875	broad.mit.edu;ucsc.edu	37	9	17457520	17457520	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CNTLN	NM_017738	exon19	c.3115-2A>G	.	.	.	81	5	81	0	.	91
CNTNAP3B	728577	broad.mit.edu;bcgsc.ca	37	9	43815876	43815877	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001201380	exon5	c.630_631insA	p.L210fs	.	.	755	9	920	0	.	.
COL14A1	7373	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	121326235	121326235	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL14A1	NM_021110	exon38	c.G4520A	p.G1507E	.	.	204	86	263	1	.	543
COL24A1	255631	bcgsc.ca	37	1	86375642	86375642	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL24A1	NM_152890	exon26	c.A2661G	p.K887K	.	.	101	5	92	0	.	94
COL6A1	1291	broad.mit.edu	37	21	47404299	47404299	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL6A1	NM_001848	exon3	c.G344C	p.S115T	.	.	50	6	92	0	.	91
COL6A5	256076	bcgsc.ca	37	3	130107771	130107771	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_153264	exon6	c.A2210G	p.D737G	.	.	118	5	132	0	.	.
COL7A1	1294	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	48608550	48608550	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	COL7A1	NM_000094	exon93	c.G7148A	p.G2383D	.	.	99	24	125	0	.	160
CPEB3	22849	bcgsc.ca	37	10	93812099	93812099	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CPEB3	NM_014912	exon10	c.T1967C	p.V656A	.	.	77	4	108	0	.	90
CPEB3	22849	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	10	93999727	93999727	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CPEB3	NM_014912	exon2	c.C381T	p.I127I	.	.	71	18	76	0	.	90
CPNE5	57699	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	36710124	36710124	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CPNE5	NM_020939	exon21	c.1703delC	p.P568fs	.	.	93	23	111	0	.	91
CR1	1378	broad.mit.edu;bcgsc.ca	37	1	207697136	207697137	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CR1	NM_000573	exon5	c.668_669insC	p.G223fs	.	.	789	10	658	0	.	93
CRISPLD2	83716	bcgsc.ca	37	16	84879399	84879399	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CRISPLD2	NM_031476	exon3	c.A248G	p.D83G	.	.	37	4	41	0	.	90
CSPG4	1464	broad.mit.edu;bcgsc.ca	37	15	75985453	75985454	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CSPG4	NM_001897	exon2	c.210_211insC	p.P70fs	.	.	197	7	288	0	.	229
CSTF1	1477	bcgsc.ca	37	20	54974025	54974025	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CSTF1	NM_001033522	exon5	c.A648G	p.E216E	.	.	271	7	268	0	.	90
CTBP1	1487	bcgsc.ca;mdanderson.org	37	4	1206151	1206151	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CTBP1	NM_001328	exon9	c.C1200T	p.I400I	.	.	57	11	92	2	.	91
CUBN	8029	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	17169924	17169924	+	Splice_Site	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CUBN	NM_001081	exon4	c.253-1G>C	.	.	.	104	23	104	0	.	166
CYFIP2	26999	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	156714055	156714055	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYFIP2	NM_001037332	exon3	c.A145G	p.R49G	.	.	182	104	102	0	.	22
CYLC1	1538	hgsc.bcm.edu;broad.mit.edu	37	X	83128980	83128981	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	CYLC1,NS,malignant_melanoma,0	CYLC1	NM_021118	exon4	c.1264_1265insA	p.E422fs	.	.	149	10	136	0	.	112
CYLC2	1539	hgsc.bcm.edu;broad.mit.edu	37	9	105767323	105767324	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYLC2	NM_001340	exon5	c.410_411insA	p.G137fs	.	.	208	13	244	0	.	91
CYP2A7	1549	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	41387943	41387943	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	CYP2A7	NM_000764	exon1	c.T173C	p.I58T	.	.	375	179	409	1	.	93
CYSTM1	84418	bcgsc.ca	37	5	139574086	139574086	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_032412	exon2	c.T36C	p.P12P	.	.	152	6	193	0	.	.
DCAF5	8816	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	69584924	69584924	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DCAF5	NM_003861	exon4	c.A467G	p.N156S	.	.	90	16	125	0	.	91
DCHS2	54798	bcgsc.ca	37	4	155298553	155298553	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DCHS2	NM_001142552	exon2	c.A2096G	p.E699G	.	.	73	4	73	0	.	94
DCHS2	54798	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	155157446	155157447	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DCHS2	NM_017639	exon25	c.6992_6993del	p.2331_2331del	.	.	227	0	191	0	.	94
DDN	23109	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	49391730	49391730	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DDN	NM_015086	exon2	c.G929C	p.G310A	.	.	100	16	101	0	.	90
DDX3X	1654	hgsc.bcm.edu	37	X	41205635	41205636	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DDX3X	NM_001356	exon13	c.1469_1470insA	p.G490fs	.	.	177	11	153	0	.	715
DDX46	9879	bcgsc.ca	37	5	134113358	134113358	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DDX46	NM_014829	exon6	c.A708G	p.K236K	.	.	134	5	97	0	.	227
DENND1C	79958	bcgsc.ca	37	19	6475543	6475543	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DENND1C	NM_024898	exon13	c.T879C	p.N293N	.	.	38	4	52	0	.	67
DGKG	1608	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	185969660	185969660	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DGKG	NM_001346	exon19	c.G1649A	p.S550N	.	.	145	28	220	0	.	714
DIAPH2	1730	bcgsc.ca	37	X	96603179	96603179	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DIAPH2	NM_007309	exon24	c.A2909G	p.K970R	.	.	231	7	256	2	.	133
DIS3L2	129563	bcgsc.ca	37	2	233103263	233103263	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DIS3L2	NM_152383	exon11	c.C1225T	p.H409Y	.	.	318	11	294	0	.	136
DLAT	1737	broad.mit.edu;bcgsc.ca	37	11	111896425	111896426	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DLAT	NM_001931	exon1	c.229_230insT	p.L77fs	.	.	93	9	114	0	.	226
DLG3	1741	bcgsc.ca	37	X	69673628	69673628	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DLG3	NM_021120	exon8	c.A1287G	p.G429G	.	.	116	7	136	0	.	219
DLK2	65989	hgsc.bcm.edu;broad.mit.edu	37	6	43418412	43418413	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DLK2	NM_206539	exon6	c.1017_1018insC	p.P339fs	.	.	143	11	182	0	.	68
DNAH10	196385	bcgsc.ca	37	12	124341763	124341763	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH10	NM_207437	exon36	c.A6245G	p.E2082G	.	.	103	5	102	0	.	95
DNAH14	127602	bcgsc.ca	37	1	225565016	225565016	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH14	NM_001373	exon77	c.T12288C	p.L4096L	.	.	447	9	350	0	.	23
DNAH2	146754	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	7701533	7701533	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH2	NM_020877	exon53	c.C8289T	p.I2763I	.	.	46	30	86	0	.	102
DNAH3	55567	bcgsc.ca	37	16	21136631	21136631	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH3	NM_017539	exon9	c.T1269C	p.A423A	.	.	193	6	136	0	.	167
DNAH5	1767	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	13727745	13727745	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH5	NM_001369	exon70	c.G11904A	p.M3968I	.	.	354	118	320	0	.	182
DNAH6	1768	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	2	84774640	84774640	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAH6	NM_001370	exon7	c.C1090T	p.R364X	.	.	358	149	353	1	.	69
DNAJC28	54943	hgsc.bcm.edu	37	21	34860757	34860757	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNAJC28	NM_001040192	exon2	c.A944T	p.N315I	.	.	360	29	470	0	.	90
DNHD1	144132	bcgsc.ca	37	11	6565371	6565371	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DNHD1	NM_144666	exon19	c.T3649C	p.S1217P	.	.	65	4	83	1	.	24
DOCK6	57572	bcgsc.ca;mdanderson.org	37	19	11348454	11348454	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DOCK6	NM_020812	exon17	c.T1834C	p.S612P	.	.	143	30	133	4	.	93
DOCK9	23348	bcgsc.ca	37	13	99532170	99532170	+	Silent	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DOCK9	NM_001130049	exon27	c.A2928T	p.I976I	.	.	83	4	109	0	.	90
DOPEY1	23033	hgsc.bcm.edu	37	6	83847672	83847673	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DOPEY1	NM_015018	exon21	c.3911_3912insA	p.R1304fs	.	.	144	11	132	0	.	155
DOT1L	84444	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	2202716	2202716	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DOT1L	NM_032482	exon9	c.A725G	p.N242S	.	.	288	198	346	0	.	132
DPM2	8818	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	130699764	130699764	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DPM2	NM_003863	exon2	c.C42T	p.V14V	.	.	129	59	147	1	.	90
DPPA2	151871	bcgsc.ca	37	3	109023454	109023454	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DPPA2	NM_138815	exon7	c.T722C	p.L241P	.	.	154	5	197	2	.	93
DPY19L1	23333	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	35050986	35050986	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DPY19L1	NM_015283	exon5	c.C407T	p.T136M	.	.	367	69	364	0	.	68
DRD5	1816	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	4	9784569	9784569	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DRD5	NM_000798	exon1	c.G916A	p.V306M	.	.	49	8	66	0	.	91
DROSHA	29102	bcgsc.ca	37	5	31410930	31410930	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DROSHA	NM_013235	exon30	c.A3590G	p.Q1197R	.	.	132	5	168	1	.	227
DSG3	1830	bcgsc.ca	37	18	29049108	29049108	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DSG3	NM_001944	exon12	c.T1693C	p.S565P	.	.	89	3	143	0	.	98
DYNC1LI2	1783	broad.mit.edu;bcgsc.ca	37	16	66761590	66761591	+	Splice_Site	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	DYNC1LI2	NM_006141	exon12	c.1261+1->A	.	.	.	65	7	80	0	.	93
EBLN2	55096	hgsc.bcm.edu;broad.mit.edu	37	3	73111508	73111509	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_018029	exon1	c.276_277insC	p.E92fs	.	.	148	11	151	0	.	.
EBLN2	55096	hgsc.bcm.edu;broad.mit.edu	37	3	73111541	73111542	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_018029	exon1	c.309_310insA	p.I103fs	.	.	195	13	231	0	.	.
ECM1	1893	bcgsc.ca	37	1	150482230	150482230	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ECM1	NM_001202858	exon3	c.A215G	p.Q72R	.	.	95	5	93	0	.	92
ECT2L	345930	bcgsc.ca	37	6	139223640	139223640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ECT2L	NM_001195037	exon21	c.T2591C	p.V864A	.	.	118	6	140	0	.	22
ELF1	1997	hgsc.bcm.edu;broad.mit.edu	37	13	41507921	41507922	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ELF1	NM_172373	exon9	c.1500_1501insG	p.G500fs	.	.	179	11	207	0	.	227
ELN	2006	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	7	73459566	73459566	+	Missense_Mutation	SNP	G	G	T	rs139718810	alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ELN	NM_001081753	exon10	c.G499T	p.G167C	.	.	59	21	48	0	G|1.000;A|0.000	95
ENDOG	2021	bcgsc.ca	37	9	131584794	131584794	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ENDOG	NM_004435	exon3	c.A799G	p.I267V	.	.	61	4	68	0	.	90
EPG5	57724	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	18	43458391	43458391	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EPG5	NM_020964	exon34	c.A5892G	p.V1964V	.	.	113	12	80	0	.	580
ERAP1	51752	hgsc.bcm.edu;broad.mit.edu	37	5	96132948	96132949	+	In_Frame_Ins	INS	-	-	TCATCTTCA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERAP1	NM_001198541	exon4	c.728_729insTGAAGATGA	p.S243delinsMKMS	.	.	239	20	281	0	.	70
ERI2	112479	hgsc.bcm.edu	37	16	20809480	20809481	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERI2	NM_001142725	exon9	c.1642_1643insA	p.Q548fs	.	.	155	11	114	0	.	153
ERI2	112479	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	20810230	20810230	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERI2	NM_001142725	exon9	c.A892G	p.I298V	.	.	605	189	427	0	.	153
ERMAP	114625	hgsc.bcm.edu;broad.mit.edu	37	1	43304572	43304573	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ERMAP	NM_018538	exon7	c.617_618insA	p.G206fs	.	.	182	12	186	0	.	91
ESCO1	114799	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	18	19112484	19112484	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ESCO1	NM_052911	exon11	c.C2325T	p.F775F	.	.	229	155	285	0	.	90
ESF1	51575	hgsc.bcm.edu	37	20	13763274	13763275	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ESF1	NM_016649	exon2	c.513_514insA	p.N171fs	.	.	437	27	356	0	.	91
ESX1	80712	bcgsc.ca	37	X	103499243	103499243	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ESX1	NM_153448	exon2	c.T98C	p.V33A	.	.	116	5	137	0	.	131
ETV3L	440695	hgsc.bcm.edu;broad.mit.edu	37	1	157067713	157067714	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ETV3L	NM_001004341	exon4	c.554_555insC	p.R185fs	.	.	184	11	169	0	.	228
EVPL	2125	broad.mit.edu;bcgsc.ca	37	17	74003866	74003867	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EVPL	NM_001988	exon22	c.5420_5421insC	p.Q1807fs	.	.	131	13	133	0	.	93
EZH1	2145	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	40871173	40871173	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	EZH1	NM_001991	exon8	c.A717G	p.A239A	.	.	325	45	266	0	.	229
F13A1	2162	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	6145912	6145912	+	Silent	SNP	G	G	A	rs200672690		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	F13A1	NM_000129	exon15	c.C2139T	p.D713D	.	.	144	61	171	0	G|0.999;A|0.001	519
F8	2157	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	154158684	154158684	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	F8	NM_000132	exon14	c.G3381C	p.W1127C	.	.	165	28	149	0	.	182
FADS6	283985	broad.mit.edu;mdanderson.org	37	17	72889516	72889516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FADS6	NM_178128	exon1	c.G178A	p.A60T	.	.	32	6	25	0	.	22
FAM107B	83641	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	14563197	14563197	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM107B	NM_031453	exon5	c.G913T	p.E305X	.	.	140	30	200	0	.	156
FAM160A2	84067	hgsc.bcm.edu;broad.mit.edu	37	11	6238840	6238841	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM160A2	NM_032127	exon9	c.2018_2019insG	p.E673fs	.	.	157	11	297	0	.	92
FAM192A	80011	bcgsc.ca	37	16	57207758	57207758	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM192A	NM_024946	exon2	c.A9G	p.G3G	.	.	154	13	235	9	.	90
FAM35A	54537	broad.mit.edu;bcgsc.ca	37	10	88912207	88912208	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAM35A	NM_019054	exon3	c.1096_1097insC	p.S366fs	.	.	843	17	857	0	.	94
FANCD2	2177	hgsc.bcm.edu;bcgsc.ca	37	3	10108913	10108913	+	Missense_Mutation	SNP	G	G	T	rs80258959	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FANCD2	NM_001018115	exon26	c.G2406T	p.Q802H	.	.	114	12	109	0	G|0.990;T|0.010	229
FANCD2	2177	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	10108898	10108898	+	Silent	SNP	A	A	G	rs77246387	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FANCD2	NM_001018115	exon26	c.A2391G	p.V797V	.	.	106	13	96	0	A|0.909;G|0.091	229
FANCM	57697	bcgsc.ca	37	14	45623968	45623968	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FANCM	NM_020937	exon7	c.T1252C	p.C418R	.	.	159	6	189	0	.	569
FASTKD1	79675	bcgsc.ca	37	2	170393801	170393801	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FASTKD1	NM_024622	exon12	c.A2124G	p.A708A	.	.	84	4	60	0	.	119
FAT2	2196	bcgsc.ca	37	5	150924557	150924557	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FAT2	NM_001447	exon9	c.A6131G	p.D2044G	.	.	134	6	128	1	.	96
FBN2	2201	bcgsc.ca	37	5	127685115	127685115	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FBN2	NM_001999	exon23	c.T2913C	p.C971C	.	.	193	6	147	0	.	146
FBXL18	80028	bcgsc.ca	37	7	5540152	5540152	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FBXL18	NM_024963	exon3	c.T1748C	p.M583T	.	.	74	5	95	0	.	651
FCGBP	8857	bcgsc.ca	37	19	40376975	40376975	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FCGBP	NM_003890	exon24	c.A11447G	p.E3816G	.	.	314	63	346	5	.	98
FCGBP	8857	hgsc.bcm.edu	37	19	40400622	40400623	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FCGBP	NM_003890	exon12	c.5467_5468insC	p.N1823fs	.	.	226	14	256	0	.	98
FCGR1C	100132417	broad.mit.edu;bcgsc.ca	37	1	149378214	149378215	+	RNA	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	99	10	82	0	.	.
FGD3	89846	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	95796931	95796931	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FGD3	NM_001083536	exon17	c.C1894T	p.P632S	.	.	73	22	112	0	.	228
FGD4	121512	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	32760995	32760995	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FGD4	NM_139241	exon8	c.G1098A	p.L366L	.	.	328	107	344	0	.	229
FILIP1L	11259	hgsc.bcm.edu;broad.mit.edu	37	3	99568989	99568990	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FILIP1L	NM_001042459	exon5	c.1531_1532insA	p.L511fs	.	.	232	15	276	0	.	45
FKBP1AP1	2282	ucsc.edu	37	19	58337923	58337923	+	RNA	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	210	20	221	0	.	.
FKBP5	2289	bcgsc.ca	37	6	35604901	35604901	+	Missense_Mutation	SNP	G	G	T	rs201013987	alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FKBP5	NM_001145775	exon4	c.C140A	p.P47Q	.	.	209	6	222	0	G|0.999;A|0.001	227
FLG2	388698	bcgsc.ca	37	1	152329184	152329184	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FLG2	NM_001014342	exon3	c.A1078G	p.N360D	.	.	159	5	114	0	.	151
FLT1	2321	bcgsc.ca	37	13	28913378	28913378	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FLT1	NM_002019	exon17	c.T2415C	p.P805P	.	.	101	5	122	0	.	1406
FRMD3	257019	bcgsc.ca	37	9	85950455	85950455	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FRMD3	NM_174938	exon6	c.T572C	p.V191A	.	.	235	6	259	0	.	91
FRY	10129	bcgsc.ca	37	13	32749684	32749684	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FRY	NM_023037	exon20	c.A2336G	p.D779G	.	.	198	6	240	1	.	142
FSIP2	401024	hgsc.bcm.edu;broad.mit.edu	37	2	186673386	186673387	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FSIP2	NM_173651	exon17	c.19620_19621insA	p.P6540fs	.	.	167	12	132	0	.	90
FUBP1	8880	hgsc.bcm.edu;ucsc.edu	37	1	78429797	78429797	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	FUBP1	NM_003902	exon12	c.C991T	p.R331X	.	.	602	219	645	0	.	227
GALNTL6	442117	bcgsc.ca	37	4	173734854	173734854	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GALNTL6	NM_001034845	exon7	c.A903G	p.A301A	.	.	68	5	117	0	.	137
GALNTL6	442117	ucsc.edu;bcgsc.ca	37	4	173804011	173804011	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GALNTL6	NM_001034845	exon8	c.C994T	p.P332S	.	.	186	82	235	3	.	137
GBAP1	2630	broad.mit.edu;bcgsc.ca	37	1	155184076	155184077	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	561	20	250	0	.	.
GBP2	2634	bcgsc.ca	37	1	89586932	89586932	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GBP2	NM_004120	exon3	c.T212C	p.V71A	.	.	208	10	243	1	.	91
GFM2	84340	hgsc.bcm.edu	37	5	74021852	74021852	+	Missense_Mutation	SNP	A	A	T	rs76339998	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GFM2	NM_032380	exon18	c.T1826A	p.F609Y	.	.	188	38	178	0	A|0.963;T|0.037	90
GLA	2717	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	100655664	100655678	+	In_Frame_Del	DEL	GGCCACATATAAAGA	GGCCACATATAAAGA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGCCACATATAAAGA	GGCCACATATAAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GLA	NM_000169	exon4	c.615_629del	p.205_210del	.	.	111	11	115	0	.	130
GLI2	2736	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	121726367	121726367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GLI2	NM_005270	exon5	c.G721A	p.A241T	.	.	94	13	132	0	.	954
GOLGA6A	342096	broad.mit.edu;bcgsc.ca	37	15	74373055	74373056	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GOLGA6A	NM_001038640	exon2	c.106_107insG	p.K36fs	.	.	1191	11	1630	0	.	44
GP6	51206	hgsc.bcm.edu	37	19	55525497	55525497	+	Missense_Mutation	SNP	A	A	G	rs1671150	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GP6	NM_001083899	exon8	c.T1816C	p.F606L	.	.	8	8	0	0	A|0.233;G|0.767	92
GP6	51206	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	55539031	55539040	+	Frame_Shift_Del	DEL	GCTGTGGGCG	GCTGTGGGCG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GCTGTGGGCG	GCTGTGGGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GP6	NM_016363	exon4	c.516_525del	p.172_175del	.	.	82	11	109	0	.	92
GPSM2	29899	hgsc.bcm.edu	37	1	109465168	109465168	+	Missense_Mutation	SNP	T	T	A	rs201481482		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GPSM2	NM_013296	exon13	c.T1570A	p.S524T	.	.	272	21	244	0	.	227
GRID1	2894	bcgsc.ca	37	10	87614325	87614325	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GRID1	NM_017551	exon8	c.T1161C	p.S387S	.	.	53	4	76	0	.	142
GRINA	2907	broad.mit.edu;bcgsc.ca	37	8	145065553	145065554	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GRINA	NM_001009184	exon2	c.162_163insC	p.Q54fs	.	.	79	8	85	0	.	90
GUCY1A2	2977	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	106810544	106810544	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GUCY1A2	NM_000855	exon4	c.C848A	p.P283Q	.	.	94	22	118	0	.	589
GUF1	60558	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	44692732	44692732	+	Splice_Site	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	GUF1	NM_021927	exon12	c.1336-2A>T	.	.	.	240	103	248	0	.	91
HBE1	3046	bcgsc.ca	37	11	5290694	5290694	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HBE1	NM_005330	exon2	c.A305G	p.E102G	.	.	189	6	193	0	.	90
HCN3	57657	hgsc.bcm.edu;bcgsc.ca	37	1	155255629	155255629	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HCN3	NM_020897	exon6	c.C1351A	p.P451T	.	.	401	36	184	0	.	154
HECW2	57520	hgsc.bcm.edu;bcgsc.ca	37	2	197183465	197183465	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HECW2	NM_020760	exon9	c.G2149C	p.D717H	.	.	127	9	163	0	.	668
HELLS	3070	hgsc.bcm.edu	37	10	96322576	96322577	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HELLS	NM_018063	exon6	c.378_379insA	p.R126fs	.	.	271	19	240	0	.	92
HEPHL1	341208	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	93822053	93822053	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HEPHL1	NM_001098672	exon12	c.C2213A	p.A738D	.	.	83	17	106	0	.	71
HEPHL1	341208	ucsc.edu;bcgsc.ca	37	11	93822054	93822054	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HEPHL1	NM_001098672	exon12	c.C2214A	p.A738A	.	.	83	17	106	1	.	71
HFM1	164045	hgsc.bcm.edu	37	1	91742605	91742605	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HFM1	NM_001017975	exon31	c.A3406C	p.K1136Q	.	.	296	13	300	0	.	112
HFM1	164045	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	91742607	91742607	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HFM1	NM_001017975	exon31	c.G3404C	p.S1135T	.	.	292	90	294	0	.	112
HFM1	164045	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	91742600	91742600	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HFM1	NM_001017975	exon31	c.3411delA	p.K1137fs	.	.	317	77	317	0	.	112
HGF	3082	bcgsc.ca	37	7	81359031	81359031	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HGF	NM_000601	exon8	c.A930G	p.G310G	.	.	142	5	114	0	.	516
HGSNAT	138050	broad.mit.edu;bcgsc.ca	37	8	43002098	43002099	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HGSNAT	NM_152419	exon2	c.126_127insA	p.D42fs	.	.	82	9	100	0	.	68
HIST1H2BM	8342	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	27782957	27782957	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIST1H2BM	NM_003521	exon1	c.C136G	p.L46V	.	.	192	76	266	0	.	131
HIST1H4D	8360	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	26189253	26189253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIST1H4D	NM_003539	exon1	c.C52T	p.R18C	.	.	75	30	64	0	.	68
HIVEP2	3097	hgsc.bcm.edu;broad.mit.edu	37	6	143094744	143094745	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HIVEP2	NM_006734	exon5	c.1132_1133insA	p.G378fs	.	.	299	18	284	0	.	95
HLA-DQB1	3119	bcgsc.ca	37	6	32632823	32632823	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HLA-DQB1	NM_002123	exon2	c.A131G	p.K44R	.	.	60	4	64	0	.	22
HLTF	6596	bcgsc.ca	37	3	148792088	148792088	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HLTF	NM_139048	exon4	c.T443C	p.M148T	.	.	146	5	125	0	.	659
HOXC10	3226	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	54382990	54382990	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HOXC10	NM_017409	exon2	c.G789A	p.L263L	.	.	200	25	220	0	.	91
HOXC8	3224	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	54404963	54404963	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HOXC8	NM_022658	exon2	c.G527C	p.R176P	.	.	116	20	105	0	.	91
HRC	3270	hgsc.bcm.edu	37	19	49657886	49657886	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HRC	NM_002152	exon1	c.G609A	p.E203E	.	.	234	10	258	0	.	91
HRNR	388697	broad.mit.edu;bcgsc.ca	37	1	152186965	152186966	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HRNR	NM_001009931	exon3	c.7140_7141insG	p.G2380fs	.	.	630	18	664	0	.	93
HSP90B1	7184	hgsc.bcm.edu	37	12	104341190	104341190	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSP90B1	NM_003299	exon17	c.A2364T	p.E788D	.	.	366	13	341	0	.	93
HSPA13	6782	bcgsc.ca	37	21	15753761	15753761	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSPA13	NM_006948	exon2	c.T129C	p.C43C	.	.	142	5	175	0	.	226
HSPB2	3316	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	111784239	111784239	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSPB2	NM_001541	exon2	c.G169A	p.G57R	.	.	50	10	54	0	.	659
HSPG2	3339	bcgsc.ca	37	1	22176644	22176644	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSPG2	NM_005529	exon57	c.T7336C	p.S2446P	.	.	67	4	128	2	.	141
HSPH1	10808	bcgsc.ca	37	13	31712659	31712659	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	HSPH1	NM_006644	exon17	c.A2255G	p.E752G	.	.	370	8	442	1	.	90
IFNA7	3444	bcgsc.ca	37	9	21202040	21202040	+	Missense_Mutation	SNP	G	G	C	rs200751233		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IFNA7	NM_021057	exon1	c.C125G	p.A42G	.	.	236	14	327	6	G|0.999;C|0.001	90
IFNA7	3444	bcgsc.ca	37	9	21202073	21202073	+	Missense_Mutation	SNP	C	C	G	rs76903863	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IFNA7	NM_021057	exon1	c.G92C	p.S31T	.	.	205	15	322	6	C|0.994;G|0.006	90
IGF1R	3480	bcgsc.ca	37	15	99460029	99460029	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IGF1R	NM_000875	exon10	c.A2125G	p.K709E	.	.	94	7	99	0	.	1490
IKBKAP	8518	bcgsc.ca	37	9	111659522	111659522	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IKBKAP	NM_003640	exon23	c.A2407G	p.S803G	.	.	115	5	140	0	.	318
IKZF5	64376	bcgsc.ca	37	10	124755639	124755639	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IKZF5	NM_001271840	exon4	c.T187C	p.L63L	.	.	58	4	94	0	.	90
IL16	3603	bcgsc.ca	37	15	81601111	81601111	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IL16	NM_172217	exon18	c.A3971G	p.K1324R	.	.	116	6	165	0	.	653
IL17C	27189	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	88705412	88705412	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IL17C	NM_013278	exon2	c.G30A	p.L10L	.	.	142	23	185	0	.	90
IL6R	3570	hgsc.bcm.edu;broad.mit.edu	37	1	154437759	154437760	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IL6R	NM_000565	exon10	c.1310_1311insG	p.L437fs	.	.	172	11	158	0	.	229
INTS10	55174	bcgsc.ca	37	8	19681410	19681410	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	INTS10	NM_018142	exon7	c.T691C	p.S231P	.	.	94	4	184	1	.	91
INTS2	57508	bcgsc.ca	37	17	59947345	59947345	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	INTS2	NM_020748	exon21	c.G2807A	p.S936N	.	.	129	27	73	6	.	206
IPO7	10527	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	9463685	9463693	+	In_Frame_Del	DEL	AACAAAGAA	AACAAAGAA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AACAAAGAA	AACAAAGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	IPO7	NM_006391	exon24	c.2960_2968del	p.987_990del	.	.	314	0	361	0	.	271
ISX	91464	bcgsc.ca	37	22	35463134	35463134	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ISX	NM_001008494	exon1	c.G54A	p.L18L	.	.	128	7	96	0	.	95
ITGAV	3685	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	187540361	187540361	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ITGAV	NM_002210	exon27	c.G2737T	p.V913F	.	.	291	88	253	0	.	653
JAG2	3714	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	14	105609430	105609430	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	JAG2	NM_002226	exon26	c.C3319T	p.R1107C	.	.	14	7	27	0	.	846
JAK2	3717	hgsc.bcm.edu;broad.mit.edu	37	9	5069192	5069193	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	JAK2	NM_004972	exon11	c.1497_1498insC	p.C499fs	.	.	178	12	195	0	.	75307
KAT6B	23522	hgsc.bcm.edu;broad.mit.edu	37	10	76735587	76735588	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_012330	exon8	c.1492_1493insC	p.T498fs	.	.	118	10	130	0	.	.
KBTBD13	390594	broad.mit.edu;bcgsc.ca;mdanderson.org	37	15	65369217	65369217	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001101362	exon1	c.C64T	p.R22C	.	.	25	14	21	0	.	.
KCNH2	3757	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	7	150671893	150671893	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNH2	NM_000238	exon2	c.G213T	p.G71G	.	.	61	17	21	0	.	94
KCNJ2	3759	bcgsc.ca	37	17	68171924	68171924	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNJ2	NM_000891	exon2	c.A744G	p.I248M	.	.	182	6	128	0	.	90
KCNK3	3777	broad.mit.edu	37	2	26915969	26915969	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNK3	NM_002246	exon1	c.G226T	p.V76L	.	.	19	5	15	0	.	91
KCNN3	3782	hgsc.bcm.edu;broad.mit.edu	37	1	154842187	154842188	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNN3	NM_001204087	exon1	c.254_255insC	p.L85fs	.	.	149	10	66	0	.	91
KCNV1	27012	mdanderson.org	37	8	110986482	110986482	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCNV1	NM_014379	exon1	c.G136T	p.G46C	.	.	19	7	11	0	.	226
KCTD4	386618	hgsc.bcm.edu;broad.mit.edu	37	13	45768382	45768383	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KCTD4	NM_198404	exon2	c.321_322insA	p.N107fs	.	.	175	11	241	0	.	90
KDM5D	8284	bcgsc.ca	37	Y	21870131	21870131	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KDM5D	NM_001146705	exon23	c.A3353G	p.E1118G	.	.	90	6	144	1	.	560
KDR	3791	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	55976873	55976873	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KDR	NM_002253	exon8	c.C1039T	p.R347C	.	.	268	113	333	0	.	2298
KIAA1147	57189	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	141362636	141362636	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1147	NM_001080392	exon9	c.A1188C	p.Q396H	.	.	118	39	99	0	.	69
KIAA1551	55196	bcgsc.ca	37	12	32134910	32134910	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_018169	exon4	c.A1021G	p.K341E	.	.	187	6	163	1	.	.
KIAA1614	57710	broad.mit.edu;bcgsc.ca	37	1	180904976	180904977	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1614	NM_020950	exon5	c.1931_1932insC	p.S644fs	.	.	77	9	60	0	.	26
KIAA1755	85449	hgsc.bcm.edu;broad.mit.edu	37	20	36869926	36869927	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA1755	NM_001029864	exon3	c.607_608insG	p.P203fs	.	.	181	11	198	0	.	95
KIAA2018	205717	bcgsc.ca	37	3	113376139	113376146	+	Frame_Shift_Del	DEL	GCTGCTGC	GCTGCTGC	-	rs71864613	alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GCTGCTGC	GCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIAA2018	NM_001009899	exon7	c.4383_4390del	p.1461_1464del	.	.	64	4	99	1	.	93
KIFC1	3833	bcgsc.ca	37	6	33374651	33374651	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KIFC1	NM_002263	exon10	c.A1976G	p.K659R	.	.	135	5	150	0	.	90
KLHL10	317719	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	40004434	40004434	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KLHL10	NM_152467	exon5	c.A1702C	p.S568R	.	.	387	200	270	0	.	227
KLHL11	55175	hgsc.bcm.edu;bcgsc.ca	37	17	40010740	40010740	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KLHL11	NM_018143	exon2	c.G1379A	p.G460E	.	.	498	45	350	0	.	90
KNTC1	9735	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	123097712	123097712	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KNTC1	NM_014708	exon54	c.T5676G	p.C1892W	.	.	177	63	158	0	.	543
KRT78	196374	broad.mit.edu;bcgsc.ca	37	12	53242576	53242577	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KRT78	NM_173352	exon1	c.139_140insG	p.C47fs	.	.	79	8	96	0	.	188
KRTAP5-1	387264	hgsc.bcm.edu;broad.mit.edu	37	11	1605983	1605984	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KRTAP5-1	NM_001005922	exon1	c.497_498insG	p.A166fs	.	.	135	11	248	0	.	44
KRTAP5-5	439915	bcgsc.ca	37	11	1651170	1651172	+	In_Frame_Del	DEL	GGC	GGC	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGC	GGC	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	KRTAP5-5	NM_001001480	exon1	c.100_102del	p.34_34del	.	.	47	7	77	0	.	23
L3MBTL2	83746	bcgsc.ca	37	22	41620741	41620741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	L3MBTL2	NM_031488	exon10	c.A1187G	p.D396G	.	.	258	9	220	2	.	92
LAMA1	284217	bcgsc.ca	37	18	6948439	6948439	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LAMA1	NM_005559	exon60	c.A8673G	p.E2891E	.	.	75	4	144	0	.	149
LAMA3	3909	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	21331052	21331052	+	Silent	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LAMA3	NM_001127717	exon5	c.G855T	p.R285R	.	.	111	28	161	0	.	100
LAMB4	22798	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	107763585	107763585	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LAMB4	NM_007356	exon2	c.T25C	p.L9L	.	.	147	60	147	0	.	140
LARP7	51574	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	113568542	113568542	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LARP7	NM_001267039	exon9	c.A855T	p.K285N	.	.	248	120	273	0	.	93
LCE1C	353133	hgsc.bcm.edu;broad.mit.edu	37	1	152777757	152777758	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LCE1C	NM_178351	exon2	c.198_199insG	p.G66fs	.	.	161	12	150	0	.	90
LCE1D	353134	hgsc.bcm.edu	37	1	152770450	152770451	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LCE1D	NM_178352	exon2	c.180_181insG	p.S60fs	.	.	128	12	131	0	.	90
LCE4A	199834	bcgsc.ca	37	1	152681693	152681698	+	In_Frame_Del	DEL	TGTGGT	TGTGGT	-	rs113617356		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	TGTGGT	TGTGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LCE4A	NM_178356	exon1	c.142_147del	p.48_49del	.	.	297	0	298	0	TGTGGT|0.500;-|0.500	90
LDLRAD2	401944	broad.mit.edu	37	1	22142444	22142444	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LDLRAD2	NM_001013693	exon3	c.G520A	p.G174S	.	.	74	4	154	0	.	90
LILRB4	11006	ucsc.edu;bcgsc.ca	37	19	55178198	55178198	+	Missense_Mutation	SNP	C	C	T	rs73933939	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LILRB4	NM_006847	exon10	c.C1039T	p.R347W	.	.	179	24	214	0	C|0.997;G|0.003	93
LOC100130015	0	bcgsc.ca	37	16	90110384	90110384	+	RNA	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	55	3	57	0	.	.
LPA	4018	bcgsc.ca	37	6	160978545	160978545	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LPA	NM_005577	exon30	c.A4690G	p.T1564A	.	.	200	6	196	0	.	74
LRP11	84918	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	150174142	150174142	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LRP11	NM_032832	exon2	c.G768A	p.M256I	.	.	146	57	199	0	.	90
LRP12	29967	hgsc.bcm.edu	37	8	105509428	105509429	+	Frame_Shift_Ins	INS	-	-	A	rs35928649		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LRP12	NM_013437	exon5	c.1352_1353insT	p.C451fs	.	.	156	11	208	0	.	90
LRRC37A2	474170	broad.mit.edu;bcgsc.ca	37	17	44626578	44626579	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001006607	exon9	c.4073_4074insT	p.A1358fs	.	.	678	23	582	0	.	.
LRRC37A	9884	broad.mit.edu;bcgsc.ca	37	17	44408811	44408812	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	LRRC37A	NM_014834	exon9	c.4168_4169insA	p.H1390fs	.	.	679	7	595	0	.	22
MAN2A2	4122	bcgsc.ca	37	15	91454416	91454416	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MAN2A2	NM_006122	exon12	c.A1891G	p.S631G	.	.	69	5	101	0	.	136
MAP2	4133	bcgsc.ca	37	2	210559520	210559520	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MAP2	NM_002374	exon7	c.A2626G	p.T876A	.	.	140	6	125	0	.	591
MBP	4155	bcgsc.ca	37	18	74696783	74696783	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MBP	NM_001025101	exon8	c.A818G	p.K273R	.	.	106	6	120	0	.	515
MC5R	4161	ucsc.edu;bcgsc.ca;mdanderson.org	37	18	13826422	13826422	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MC5R	NM_005913	exon1	c.G658A	p.A220T	.	.	138	42	214	1	.	526
MCFD2	90411	bcgsc.ca	37	2	47136279	47136279	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MCFD2	NM_001171506	exon3	c.T32C	p.F11S	.	.	159	5	178	0	.	90
MCM3AP	8888	bcgsc.ca	37	21	47662726	47662726	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MCM3AP	NM_003906	exon25	c.A5416G	p.R1806G	.	.	218	6	262	0	.	291
MED12L	116931	broad.mit.edu;bcgsc.ca	37	3	151148162	151148163	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MED12L	NM_053002	exon42	c.6379_6380insT	p.L2127fs	.	.	72	7	94	0	.	576
MEF2A	4205	broad.mit.edu;bcgsc.ca	37	15	100252792	100252792	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MEF2A	NM_005587	exon11	c.G1316T	p.R439L	.	.	36	7	51	0	.	455
MEMO1	51072	bcgsc.ca	37	2	32143092	32143092	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MEMO1	NM_015955	exon5	c.T340C	p.W114R	.	.	79	4	57	0	.	92
MFF	56947	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	228220420	228220420	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MFF	NM_020194	exon10	c.C840T	p.T280T	.	.	372	127	350	0	.	153
MFHAS1	9258	bcgsc.ca	37	8	8749244	8749244	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MFHAS1	NM_004225	exon1	c.A1325G	p.D442G	.	.	27	4	65	1	.	90
MIER1	57708	bcgsc.ca	37	1	67450540	67450540	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MIER1	NM_001077700	exon14	c.T1655C	p.V552A	.	.	208	6	218	0	.	91
MIR122	406906	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	56118310	56118312	+	RNA	DEL	AGC	AGC	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	71	39	133	0	.	.
MIR92B	693235	hgsc.bcm.edu;broad.mit.edu	37	1	155165011	155165012	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	263	17	46	0	.	.
MLEC	9761	broad.mit.edu;bcgsc.ca	37	12	121134204	121134205	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MLEC	NM_014730	exon5	c.735_736insA	p.L245fs	.	.	68	7	83	0	.	91
MLL2	8085	hgsc.bcm.edu;broad.mit.edu	37	12	49425625	49425626	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MLL2	NM_003482	exon39	c.12863_12864insC	p.R4288fs	.	.	165	11	239	0	.	612
MSLN	10232	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	812697	812697	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MSLN	NM_005823	exon3	c.C17G	p.A6G	.	.	159	29	131	0	.	91
MTERFD3	80298	bcgsc.ca	37	12	107371766	107371766	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MTERFD3	NM_001033050	exon3	c.G727A	p.E243K	.	.	160	5	153	0	.	68
MTOR	2475	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11303173	11303173	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MTOR	NM_004958	exon9	c.T1410C	p.H470H	.	.	40	24	67	0	.	1439
MUC13	56667	bcgsc.ca	37	3	124646643	124646643	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MUC13	NM_033049	exon2	c.A247T	p.T83S	.	.	216	9	320	3	.	90
MUC17	140453	bcgsc.ca	37	7	100685676	100685676	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MUC17	NM_001040105	exon3	c.T10979C	p.V3660A	.	.	137	5	157	0	.	95
MYH2	4620	bcgsc.ca	37	17	10428806	10428806	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYH2	NM_017534	exon32	c.A4499G	p.Q1500R	.	.	154	5	245	0	.	194
MYL4	4635	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	45299202	45299202	+	Silent	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYL4	NM_001002841	exon5	c.G468C	p.R156R	.	.	167	83	144	0	.	92
MYO10	4651	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	16701663	16701663	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYO10	NM_012334	exon25	c.C2841T	p.F947F	.	.	83	33	114	0	.	3
MYO15A	51168	bcgsc.ca	37	17	18022794	18022794	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYO15A	NM_016239	exon2	c.A680G	p.E227G	.	.	63	4	58	0	.	97
MYO5B	4645	bcgsc.ca	37	18	47421378	47421378	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYO5B	NM_001080467	exon22	c.A2978G	p.Q993R	.	.	138	5	202	1	.	72
MYOCD	93649	bcgsc.ca	37	17	12666431	12666431	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYOCD	NM_001146312	exon14	c.A2431G	p.K811E	.	.	47	4	75	0	.	93
MYPN	84665	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	69881741	69881741	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	MYPN	NM_001256267	exon3	c.G546T	p.K182N	.	.	85	22	111	0	.	95
NANOGNB	360030	hgsc.bcm.edu;broad.mit.edu	37	12	7922711	7922712	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145465	exon2	c.235_236insA	p.E79fs	.	.	163	10	156	0	.	.
NAPA	8775	hgsc.bcm.edu;broad.mit.edu	37	19	47995348	47995349	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NAPA	NM_003827	exon8	c.590_591insC	p.L197fs	.	.	158	13	145	0	.	90
NBAS	51594	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	15519748	15519748	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NBAS	NM_015909	exon30	c.G3568T	p.D1190Y	.	.	334	44	337	0	.	94
NBPF10	100132406	broad.mit.edu;bcgsc.ca	37	1	145368590	145368591	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001039703	exon84	c.10568_10569insC	p.I3523fs	.	.	1793	12	1701	0	.	.
NBPF9	400818	bcgsc.ca	37	1	144618181	144618181	+	RNA	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	363	40	369	1	.	.
NBR1	4077	hgsc.bcm.edu	37	17	41352494	41352495	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NBR1	NM_031862	exon17	c.2337_2338insG	p.A779fs	.	.	93	9	76	0	.	130
NCOA1	8648	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	2	24991260	24991260	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NCOA1	NM_003743	exon21	c.A4326T	p.X1442Y	.	.	81	17	102	0	.	228
NELFCD	51497	bcgsc.ca	37	20	57566383	57566383	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_198976	exon9	c.T1025C	p.F342S	.	.	144	5	130	1	.	.
NELFE	7936	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	31921602	31921602	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_002904	exon10	c.G949C	p.G317R	.	.	327	65	251	0	.	.
NFATC3	4775	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	16	68224766	68224766	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NFATC3	NM_173163	exon9	c.G2194C	p.D732H	.	.	185	14	217	0	.	92
NFKB2	4791	bcgsc.ca	37	10	104156678	104156678	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NFKB2	NM_002502	exon6	c.A261G	p.G87G	.	.	75	5	97	0	.	522
NGF	4803	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	115829018	115829018	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NGF	NM_002506	exon3	c.C399T	p.F133F	.	.	144	60	158	0	.	1083
NHSL2	340527	bcgsc.ca	37	X	71358969	71358969	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NHSL2	NM_001013627	exon6	c.T1571C	p.L524P	.	.	70	4	68	0	.	108
NKTR	4820	hgsc.bcm.edu	37	3	42679763	42679764	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NKTR	NM_005385	exon13	c.2567_2568insA	p.S856fs	.	.	205	15	193	0	.	93
NLGN1	22871	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	173998709	173998709	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLGN1	NM_014932	exon7	c.C2088T	p.A696A	.	.	121	56	142	0	.	231
NLRP11	204801	bcgsc.ca	37	19	56321646	56321646	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLRP11	NM_145007	exon5	c.T330C	p.S110S	.	.	260	7	218	0	.	169
NLRP1	22861	hgsc.bcm.edu;broad.mit.edu	37	17	5462267	5462268	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLRP1	NM_014922	exon4	c.1749_1750insA	p.K583fs	.	.	158	11	219	0	.	274
NLRP2	55655	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	55508705	55508705	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NLRP2	NM_017852	exon12	c.C2900G	p.P967R	.	.	319	96	313	0	.	120
NR2C1	7181	bcgsc.ca	37	12	95456462	95456462	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NR2C1	NM_001032287	exon3	c.A107G	p.D36G	.	.	135	6	132	1	.	187
NT5C1B-RDH14	100526794	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	18736770	18736770	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001199103	exon9	c.G1640A	p.R547H	.	.	187	33	146	0	.	.
NUDT17	200035	hgsc.bcm.edu;broad.mit.edu	37	1	145587383	145587384	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NUDT17	NM_001012758	exon6	c.697_698insC	p.G233fs	.	.	127	10	97	0	.	90
NUMA1	4926	bcgsc.ca	37	11	71726847	71726847	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NUMA1	NM_006185	exon15	c.A1702G	p.K568E	.	.	178	6	241	1	.	633
NXPH1	30010	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	8791057	8791057	+	Silent	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	NXPH1	NM_152745	exon3	c.T474A	p.T158T	.	.	144	41	128	0	.	69
OR10A2	341276	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	6891840	6891840	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR10A2	NM_001004460	exon1	c.G855T	p.K285N	.	.	127	43	202	0	.	113
OR10A7	121364	broad.mit.edu;bcgsc.ca	37	12	55614789	55614810	+	Frame_Shift_Del	DEL	GAGAGAAACTCATCTAAGATAT	GAGAGAAACTCATCTAAGATAT	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GAGAGAAACTCATCTAAGATAT	GAGAGAAACTCATCTAAGATAT	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR10A7	NM_001005280	wholegene			.	.	243	0	227	0	.	72
OR2A12	346525	hgsc.bcm.edu;broad.mit.edu	37	7	143792820	143792821	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2A12	NM_001004135	exon1	c.620_621insG	p.V207fs	.	.	143	11	133	0	.	92
OR2B11	127623	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	247614658	247614658	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2B11	NM_001004492	exon1	c.C627A	p.F209L	.	.	111	34	93	0	.	69
OR2C1	4993	hgsc.bcm.edu;bcgsc.ca	37	16	3406154	3406154	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2C1	NM_012368	exon1	c.G214A	p.A72T	.	.	520	34	292	0	.	69
OR2W5	441932	hgsc.bcm.edu;bcgsc.ca	37	1	247655276	247655276	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR2W5	NM_001004698	exon1	c.T847C	p.S283P	.	.	293	11	224	0	.	115
OR4C45	403257	bcgsc.ca	37	11	48367075	48367075	+	RNA	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	155	7	208	0	.	.
OR52K1	390036	bcgsc.ca	37	11	4510358	4510358	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR52K1	NM_001005171	exon1	c.T228C	p.S76S	.	.	205	6	299	0	.	68
OR5D13	390142	hgsc.bcm.edu;ucsc.edu	37	11	55541187	55541187	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR5D13	NM_001001967	exon1	c.A274T	p.R92X	.	.	525	110	638	0	.	71
OR5D16	390144	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	55606431	55606431	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR5D16	NM_001005496	exon1	c.C204A	p.L68L	.	.	407	89	511	0	.	73
OR6C4	341418	hgsc.bcm.edu;broad.mit.edu	37	12	55945306	55945307	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6C4	NM_001005494	exon1	c.296_297insT	p.Y99fs	.	.	218	18	206	0	.	68
OR6S1	341799	broad.mit.edu;bcgsc.ca	37	14	21109759	21109760	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6S1	NM_001001968	exon1	c.92_93insT	p.S31fs	.	.	74	8	103	0	.	70
OR6X1	390260	hgsc.bcm.edu;broad.mit.edu	37	11	123624382	123624383	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OR6X1	NM_001005188	exon1	c.845_846insC	p.L282fs	.	.	144	10	168	0	.	71
ORC1	4998	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	1	52859445	52859445	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ORC1	NM_004153	exon6	c.C752A	p.T251N	.	.	104	39	70	0	.	206
OTOF	9381	bcgsc.ca	37	2	26699869	26699869	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OTOF	NM_194248	exon22	c.A2566G	p.N856D	.	.	131	5	150	0	.	135
OTP	23440	ucsc.edu;bcgsc.ca;mdanderson.org	37	5	76932769	76932769	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OTP	NM_032109	exon2	c.G324C	p.R108R	.	.	97	14	111	1	.	69
OXTR	5021	mdanderson.org	37	3	8809175	8809175	+	Silent	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	OXTR	NM_000916	exon3	c.C699G	p.L233L	.	.	30	5	38	0	.	68
PA2G4	5036	bcgsc.ca;mdanderson.org	37	12	56500791	56500791	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PA2G4	NM_006191	exon3	c.A235G	p.S79G	.	.	300	42	316	1	.	68
PAN2	9924	bcgsc.ca	37	12	56720479	56720479	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PAN2	NM_014871	exon7	c.T1184C	p.L395P	.	.	116	5	138	0	.	702
PANK4	55229	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	2452651	2452651	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PANK4	NM_018216	exon3	c.G311C	p.C104S	.	.	312	54	299	0	.	158
PARD3	56288	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	34400172	34400172	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PARD3	NM_019619	exon25	c.G3996A	p.V1332V	.	.	101	53	150	0	.	92
PCDH15	65217	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	10	56128943	56128943	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCDH15	NM_001142763	exon6	c.G426A	p.V142V	.	.	136	24	162	0	.	193
PCDHA9	9752	hgsc.bcm.edu	37	5	140230508	140230509	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCDHA9	NM_014005	exon1	c.2428_2429insT	p.I810fs	.	.	279	24	126	0	.	138
PCDHGA10	56106	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140793274	140793274	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_032090	exon1	c.C532T	p.P178S	.	.	72	13	72	0	.	.
PCDHGC3	5098	hgsc.bcm.edu;bcgsc.ca	37	5	140855947	140855947	+	Silent	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCDHGC3	NM_032402	exon1	c.G264C	p.V88V	.	.	175	27	168	0	.	24
PCNT	5116	bcgsc.ca	37	21	47746456	47746456	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCNT	NM_006031	exon2	c.T220C	p.S74P	.	.	122	6	171	0	.	141
PCNT	5116	hgsc.bcm.edu;broad.mit.edu	37	21	47819683	47819684	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCNT	NM_006031	exon25	c.4764_4765insA	p.Q1588fs	.	.	207	13	237	0	.	141
PCNXL2	80003	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	233137318	233137318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PCNXL2	NM_014801	exon29	c.G5062A	p.A1688T	.	.	354	89	313	1	.	91
PDCD1LG2	80380	bcgsc.ca	37	9	5534753	5534753	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PDCD1LG2	NM_025239	exon3	c.A64G	p.T22A	.	.	72	4	89	0	.	227
PDLIM2	64236	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	8	22438952	22438952	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PDLIM2	NM_021630	exon3	c.A904G	p.I302V	.	.	82	25	261	0	.	90
PDZD2	23037	hgsc.bcm.edu	37	5	32058103	32058104	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PDZD2	NM_178140	exon11	c.2094_2095insG	p.S698fs	.	.	201	14	223	0	.	563
PELI2	57161	bcgsc.ca	37	14	56746466	56746466	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PELI2	NM_021255	exon3	c.A280G	p.T94A	.	.	60	4	46	0	.	91
PGAM1	5223	broad.mit.edu;bcgsc.ca	37	10	99190813	99190814	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PGAM1	NM_002629	exon3	c.516_517insC	p.V172fs	.	.	262	11	340	0	.	226
PGBD3	267004	bcgsc.ca	37	10	50724169	50724169	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PGBD3	NM_170753	exon2	c.T992C	p.L331P	.	.	123	7	128	0	.	109
PI4KAP2	375133	hgsc.bcm.edu;broad.mit.edu	37	22	21838338	21838339	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PI4KAP2	.	.	.	.	.	.	138	12	115	0	.	68
PIAS4	51588	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	19	4037690	4037690	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PIAS4	NM_015897	exon11	c.C1350T	p.G450G	.	.	68	37	33	0	.	659
PIK3CA	5290	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	178936091	178936091	+	Missense_Mutation	SNP	G	G	A	rs104886003	bycluster	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	PIK3CA,bladder,carcinoma,0	PIK3CA	NM_006218	exon10	c.G1633A	p.E545K	.	.	460	90	497	1	.	27752
PJA1	64219	hgsc.bcm.edu;broad.mit.edu	37	X	68382256	68382257	+	Nonsense_Mutation	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PJA1	NM_145119	exon2	c.826_827insT	p.D276_T277delinsX	.	.	152	11	127	0	.	130
PLCB2	5330	bcgsc.ca	37	15	40590447	40590447	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLCB2	NM_004573	exon11	c.A1132G	p.M378V	.	.	69	4	126	0	.	275
PLCG1	5335	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	39794969	39794969	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLCG1	NM_182811	exon17	c.C1935T	p.R645R	.	.	95	18	119	0	.	911
PLCH1	23007	hgsc.bcm.edu;broad.mit.edu	37	3	155200477	155200478	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLCH1	NM_001130960	exon23	c.3362_3363insA	p.S1121fs	.	.	183	11	210	0	.	151
PLEKHA4	57664	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	49364948	49364948	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA4	NM_001161354	exon4	c.A194G	p.D65G	.	.	77	29	68	0	.	227
PLEKHA5	54477	hgsc.bcm.edu;broad.mit.edu	37	12	19427544	19427545	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA5	NM_001256470	exon11	c.940_941insA	p.Q314fs	.	.	145	10	133	0	.	227
PLEKHA8P1	51054	hgsc.bcm.edu;broad.mit.edu	37	12	45567240	45567241	+	RNA	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLEKHA8P1	.	.	.	.	.	.	163	10	180	0	.	226
PLXNA2	5362	bcgsc.ca	37	1	208225798	208225798	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PLXNA2	NM_025179	exon15	c.T2867C	p.V956A	.	.	77	4	55	0	.	92
POGZ	23126	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	151413427	151413427	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	POGZ	NM_145796	exon3	c.T260G	p.V87G	.	.	459	50	404	1	.	93
POP1	10940	hgsc.bcm.edu	37	8	99148886	99148887	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	POP1	NM_001145860	exon8	c.1188_1189insA	p.I396fs	.	.	149	11	139	0	.	154
POT1	25913	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	124464094	124464094	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	POT1	NM_015450	exon19	c.A1827G	p.S609S	.	.	304	114	262	0	.	227
POTEM	641455	hgsc.bcm.edu	37	14	20019862	20019863	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145442	exon1	c.359_360insT	p.W120fs	.	.	119	22	138	0	.	.
PPIP5K2	23262	bcgsc.ca	37	5	102474108	102474108	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PPIP5K2	NM_015216	exon4	c.T422C	p.L141P	.	.	257	7	174	2	.	92
PPP6C	5537	bcgsc.ca	37	9	127915914	127915914	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PPP6C	NM_001123355	exon7	c.A678G	p.G226G	.	.	85	4	109	0	.	227
PRAMEF9	343070	hgsc.bcm.edu	37	1	13427643	13427644	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001010890	exon4	c.1221_1222insA	p.L407fs	.	.	133	11	233	0	.	.
PRDX2	7001	hgsc.bcm.edu;broad.mit.edu	37	19	12911099	12911100	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRDX2	NM_005809	exon4	c.272_273insC	p.I91fs	.	.	184	11	212	0	.	90
PRNP	5621	broad.mit.edu;bcgsc.ca	37	20	4680180	4680181	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRNP	NM_001080121	exon2	c.314_315insA	p.P105fs	.	.	68	7	84	0	.	514
PROSC	11212	bcgsc.ca	37	8	37632913	37632913	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PROSC	NM_007198	exon6	c.A511G	p.K171E	.	.	86	4	130	0	.	90
PRPF39	55015	hgsc.bcm.edu;broad.mit.edu	37	14	45564691	45564692	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRPF39	NM_017922	exon2	c.249_250insT	p.K83fs	.	.	166	10	176	0	.	70
PRPF40A	55660	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	153529052	153529052	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRPF40A	NM_017892	exon13	c.T1291A	p.S431T	.	.	259	89	247	0	.	68
PRPF8	10594	bcgsc.ca	37	17	1585287	1585287	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRPF8	NM_006445	exon5	c.T480C	p.H160H	.	.	55	4	106	0	.	525
PRSS3	5646	bcgsc.ca	37	9	33797861	33797861	+	Missense_Mutation	SNP	A	A	G	rs151192741	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PRSS3	NM_007343	exon3	c.A406G	p.K136E	.	.	193	33	295	24	A|0.999;G|0.001	90
PSMD13	5719	hgsc.bcm.edu	37	11	244104	244105	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PSMD13	NM_175932	exon2	c.159_160insG	p.F53fs	.	.	154	10	180	0	.	515
PTEN	5728	hgsc.bcm.edu;broad.mit.edu	37	10	89720665	89720666	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	PTEN,NS,carcinoma,+2	PTEN	NM_000314	exon8	c.816_817insT	p.H272fs	.	.	218	16	139	0	.	17735
PTK6	5753	ucsc.edu;mdanderson.org	37	20	62162199	62162199	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTK6	NM_005975	exon6	c.C914A	p.S305X	.	.	236	39	219	1	.	419
PTMS	5763	bcgsc.ca	37	12	6878828	6878828	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTMS	NM_002824	exon2	c.A105G	p.K35K	.	.	98	4	113	0	.	91
PTPN12	5782	broad.mit.edu;bcgsc.ca	37	7	77247882	77247883	+	Frame_Shift_Ins	INS	-	-	GT	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTPN12	NM_002835	exon12	c.1025_1026insGT	p.S342fs	.	.	71	7	66	0	.	228
PTPN21	11099	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	14	88938677	88938677	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PTPN21	NM_007039	exon15	c.C2782T	p.Q928X	.	.	284	51	358	0	.	230
PXDN	7837	broad.mit.edu;bcgsc.ca	37	2	1652251	1652251	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PXDN	NM_012293	exon17	c.G3301A	p.A1101T	.	.	34	6	73	0	.	166
PYGM	5837	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	64517976	64517976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	PYGM	NM_005609	exon17	c.G2049A	p.M683I	.	.	138	24	177	0	.	92
QTRTD1	79691	bcgsc.ca	37	3	113795600	113795600	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	QTRTD1	NM_001256835	exon6	c.A593G	p.K198R	.	.	140	5	211	1	.	91
R3HDM1	23518	bcgsc.ca;mdanderson.org	37	2	136409526	136409526	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	R3HDM1	NM_015361	exon17	c.G1847C	p.G616A	.	.	176	34	184	0	.	91
RABGGTA	5875	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	24738189	24738189	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_004581	exon7	c.G726A	p.Q242Q	.	.	128	29	150	0	.	.
RACGAP1P	83956	bcgsc.ca	37	12	45458193	45458193	+	RNA	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	117	5	88	0	.	.
RAD50	10111	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	5	131924503	131924503	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD50	NM_005732	exon8	c.G1176T	p.Q392H	.	.	524	47	400	0	.	229
RAD51	5888	hgsc.bcm.edu;broad.mit.edu	37	15	41022163	41022164	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD51	NM_001164269	exon9	c.890_891insA	p.S297fs	.	.	164	10	185	0	.	563
RAD52	5893	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	1023279	1023279	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAD52	NM_134424	exon11	c.G976C	p.E326Q	.	.	125	18	144	0	.	227
RANBP9	10048	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	13657454	13657454	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RANBP9	NM_005493	exon4	c.C791G	p.S264C	.	.	211	23	223	0	.	414
RAPGEF1	2889	hgsc.bcm.edu;broad.mit.edu	37	9	134501450	134501451	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RAPGEF1	NM_198679	exon10	c.1564_1565insC	p.Y522fs	.	.	157	10	199	0	.	849
RASA2	5922	bcgsc.ca	37	3	141206040	141206040	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RASA2	NM_006506	exon1	c.A115G	p.S39G	.	.	85	5	123	3	.	661
RASGRF1	5923	bcgsc.ca	37	15	79350761	79350761	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RASGRF1	NM_001145648	exon3	c.T446C	p.I149T	.	.	159	5	214	0	.	662
RBL1	5933	bcgsc.ca	37	20	35690576	35690576	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RBL1	NM_183404	exon8	c.A994G	p.T332A	.	.	408	11	352	0	.	419
RBL2	5934	hgsc.bcm.edu;broad.mit.edu	37	16	53513829	53513830	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RBL2	NM_005611	exon19	c.2807_2808insA	p.R936fs	.	.	151	10	269	0	.	841
RBM26	64062	bcgsc.ca	37	13	79894795	79894795	+	Silent	SNP	T	T	C	rs146868835	alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RBM26	NM_022118	exon21	c.A2904G	p.E968E	.	.	178	6	222	0	T|1.000;A|0.000	91
RBMXL1	494115	bcgsc.ca	37	1	89449751	89449751	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	82	4	75	0	.	.
RBMXL3	139804	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	114426299	114426299	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145346	exon1	c.C2295T	p.D765D	.	.	50	36	113	0	.	.
RBPMS	11030	bcgsc.ca	37	8	30242626	30242626	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RBPMS	NM_006867	exon1	c.A18G	p.K6K	.	.	49	7	52	0	.	91
REG1P	5969	broad.mit.edu	37	2	79364258	79364258	+	RNA	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	26	9	35	0	.	.
REV3L	5980	bcgsc.ca	37	6	111695790	111695790	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	REV3L	NM_002912	exon13	c.A3768G	p.G1256G	.	.	105	4	86	0	.	294
RGS4	5999	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	163039295	163039295	+	Silent	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RGS4	NM_001102445	exon2	c.T312A	p.G104G	.	.	146	23	140	0	.	652
RGS7	6000	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	240976967	240976967	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RGS7	NM_002924	exon13	c.T907G	p.S303A	.	.	148	71	105	0	.	232
RIF1	55183	bcgsc.ca	37	2	152285348	152285348	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RIF1	NM_018151	exon9	c.A837G	p.E279E	.	.	201	8	172	0	.	300
RIMS3	9783	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	41092203	41092203	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RIMS3	NM_014747	exon8	c.C913T	p.P305S	.	.	51	9	82	0	.	90
RIN1	9610	bcgsc.ca	37	11	66100034	66100034	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RIN1	NM_004292	exon10	c.C2065G	p.L689V	.	.	66	21	93	0	.	710
RING1	6015	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	33177781	33177781	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	RING1,NS,carcinoma,0	RING1	NM_002931	exon4	c.T329G	p.I110S	.	.	132	39	102	0	.	159
RNASEH2A	10535	broad.mit.edu;bcgsc.ca	37	19	12918138	12918139	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNASEH2A	NM_006397	exon3	c.318_319insG	p.L106fs	.	.	69	7	75	0	.	524
RNF166	115992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	88766049	88766049	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF166	NM_178841	exon3	c.C404A	p.P135H	.	.	94	52	135	0	.	226
RNF213	57674	bcgsc.ca	37	17	78321647	78321647	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF213	NM_001256071	exon29	c.A9512G	p.K3171R	.	.	130	6	95	0	.	577
RNF26	79102	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	11	119206969	119206969	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF26	NM_032015	exon1	c.G1137C	p.K379N	.	.	61	9	82	0	.	227
RNF44	22838	bcgsc.ca	37	5	175957957	175957957	+	Silent	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF44	NM_014901	exon5	c.C531A	p.S177S	.	.	76	20	68	1	.	658
RNF44	22838	hgsc.bcm.edu;bcgsc.ca	37	5	175957958	175957958	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RNF44	NM_014901	exon5	c.C530A	p.S177Y	.	.	76	20	70	0	.	658
RNU6-71	100873774	hgsc.bcm.edu;broad.mit.edu	37	6	56472828	56472829	+	RNA	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	191	14	153	0	.	.
RP1	6101	hgsc.bcm.edu;broad.mit.edu	37	8	55542461	55542462	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RP1	NM_006269	exon4	c.6019_6020insA	p.Q2007fs	.	.	188	13	208	0	.	102
RPL10A	4736	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	6	35437288	35437288	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RPL10A	NM_007104	exon4	c.A292C	p.K98Q	.	.	72	23	71	0	.	91
RPL36A-HNRNPH2	0	hgsc.bcm.edu;broad.mit.edu	37	X	100646804	100646805	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001199973	exon3	c.279_280insA	p.R93fs	.	.	153	10	196	0	.	.
RPL5	6125	bcgsc.ca	37	1	93306110	93306110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RPL5	NM_000969	exon7	c.G708A	p.M236I	.	.	69	4	67	0	.	90
RPRD2	23248	bcgsc.ca	37	1	150445344	150445344	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RPRD2	NM_015203	exon11	c.T3920C	p.F1307S	.	.	302	35	299	24	.	23
RRN3	54700	broad.mit.edu;bcgsc.ca	37	16	15164034	15164035	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RRN3	NM_018427	exon14	c.1337_1338insG	p.A446fs	.	.	714	7	757	0	.	91
RRNAD1	51093	ucsc.edu	37	1	156703904	156703904	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RRNAD1	NM_015997	exon6	c.A740G	p.Q247R	.	.	169	1	127	1	.	90
RRP12	23223	hgsc.bcm.edu;broad.mit.edu	37	10	99116875	99116876	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RRP12	NM_015179	exon34	c.3870_3871insA	p.N1290fs	.	.	118	11	104	0	.	92
RTEL1	51750	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	62326478	62326478	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RTEL1	NM_032957	exon33	c.C3475G	p.L1159V	.	.	44	6	43	0	.	44
RXFP3	51289	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	33937720	33937720	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RXFP3	NM_016568	exon1	c.G875A	p.R292H	.	.	151	67	117	0	.	91
RXFP4	339403	hgsc.bcm.edu;broad.mit.edu	37	1	155912224	155912225	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RXFP4	NM_181885	exon1	c.724_725insG	p.R242fs	.	.	158	10	149	0	.	90
RYR2	6262	ucsc.edu;bcgsc.ca	37	1	237433796	237433796	+	Splice_Site	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	RYR2	NM_001035	exon2	c.49-1G>C	.	.	.	525	63	438	1	.	158
SAMD15	161394	hgsc.bcm.edu;broad.mit.edu	37	14	77844867	77844868	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SAMD15	NM_001010860	exon1	c.1106_1107insG	p.E369fs	.	.	215	18	222	0	.	90
SBNO1	55206	ucsc.edu	37	12	123808330	123808330	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SBNO1	NM_001167856	exon15	c.G2022A	p.R674R	.	.	72	1	64	0	.	292
SCAP	22937	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	3	47476584	47476584	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SCAP	NM_012235	exon3	c.G166T	p.E56X	.	.	108	24	167	0	.	91
SCGB2A2	4250	bcgsc.ca	37	11	62038409	62038409	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SCGB2A2	NM_002411	exon2	c.T112C	p.S38P	.	.	129	5	175	0	.	91
SCIN	85477	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	12666376	12666376	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SCIN	NM_001112706	exon8	c.G1149T	p.Q383H	.	.	296	105	269	0	.	24
SENP3	26168	hgsc.bcm.edu;ucsc.edu	37	17	7470288	7470288	+	Missense_Mutation	SNP	A	A	G	rs76586164		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SENP3	NM_015670	exon8	c.A1307G	p.K436R	.	.	209	20	405	0	A|0.500;G|0.500	659
SENP6	26054	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	6	76386875	76386875	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SENP6	NM_015571	exon14	c.C1751G	p.P584R	.	.	514	162	399	1	.	660
SERPINB10	5273	bcgsc.ca	37	18	61585292	61585292	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SERPINB10	NM_005024	exon3	c.A328C	p.T110P	.	.	152	32	160	5	.	227
SETD2	29072	bcgsc.ca	37	3	47098364	47098364	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SETD2	NM_014159	exon15	c.A6910G	p.T2304A	.	.	289	8	339	0	.	1273
SETD6	79918	broad.mit.edu	37	16	58549701	58549701	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SETD6	NM_024860	exon2	c.G34A	p.G12R	.	.	31	5	45	0	.	91
SFSWAP	6433	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	132204080	132204080	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SFSWAP	NM_001261411	exon4	c.A602T	p.E201V	.	.	362	81	215	0	.	91
SGSM2	9905	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	2282729	2282729	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SGSM2	NM_014853	exon24	c.G3071A	p.R1024H	.	.	126	19	161	1	.	68
SHMT1	6470	bcgsc.ca	37	17	18251750	18251750	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SHMT1	NM_148918	exon4	c.T247C	p.Y83H	.	.	71	5	96	0	.	91
SHOX2	6474	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	3	157823590	157823590	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SHOX2	NM_003030	exon1	c.G224T	p.G75V	.	.	19	13	21	0	.	90
SIDT2	51092	ucsc.edu;bcgsc.ca;mdanderson.org	37	11	117053474	117053474	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SIDT2	NM_001040455	exon6	c.C654T	p.F218F	.	.	108	25	136	2	.	90
SLC22A25	387601	bcgsc.ca	37	11	62984792	62984792	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC22A25	NM_199352	exon4	c.T824C	p.F275S	.	.	55	4	67	0	.	72
SLC22A8	9376	broad.mit.edu;bcgsc.ca	37	11	62767298	62767299	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC22A8	NM_001184732	exon4	c.454_455insC	p.I152fs	.	.	77	9	103	0	.	93
SLC24A5	283652	ucsc.edu;bcgsc.ca	37	15	48426509	48426509	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC24A5	NM_205850	exon3	c.C356T	p.S119L	.	.	230	47	313	7	.	90
SLC25A3	5250	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	98991699	98991699	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC25A3	NM_005888	exon4	c.T348C	p.V116V	.	.	458	172	410	0	.	90
SLC38A10	124565	hgsc.bcm.edu;broad.mit.edu	37	17	79226065	79226066	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC38A10	NM_001037984	exon13	c.1875_1876insA	p.K625fs	.	.	132	12	114	0	.	70
SLC6A17	388662	bcgsc.ca	37	1	110714700	110714700	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC6A17	NM_001010898	exon3	c.A305G	p.Y102C	.	.	152	8	188	1	.	92
SLC7A13	157724	bcgsc.ca	37	8	87229847	87229847	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLC7A13	NM_138817	exon3	c.T1031C	p.V344A	.	.	191	6	178	2	.	90
SLCO1A2	6579	hgsc.bcm.edu	37	12	21453394	21453395	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLCO1A2	NM_021094	exon7	c.798_799insT	p.L266fs	.	.	214	13	188	0	.	157
SLCO1B1	10599	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	21329794	21329794	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SLCO1B1	NM_006446	exon5	c.A444G	p.L148L	.	.	266	80	274	0	.	97
SMAD7	4092	bcgsc.ca	37	18	46448217	46448217	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMAD7	NM_005904	exon4	c.A806G	p.E269G	.	.	74	4	50	0	.	414
SMARCA2	6595	bcgsc.ca	37	9	2058353	2058353	+	Silent	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMARCA2	NM_139045	exon8	c.C1410A	p.A470A	.	.	90	4	84	0	.	653
SMARCA2	6595	bcgsc.ca	37	9	2181597	2181597	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMARCA2	NM_003070	exon30	c.T4280C	p.F1427S	.	.	123	5	202	1	.	653
SMARCA4	6597	bcgsc.ca;mdanderson.org	37	19	11098360	11098360	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMARCA4	NM_003072	exon6	c.C878T	p.A293V	.	.	186	58	212	1	.	1523
SMG1	23049	bcgsc.ca	37	16	18860698	18860698	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMG1	NM_015092	exon36	c.A5464G	p.I1822V	.	.	91	6	81	0	.	1160
SMNDC1	10285	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	10	112053908	112053908	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SMNDC1	NM_005871	exon6	c.A717G	p.X239X	.	.	132	54	159	0	.	91
SNAPC2	6618	bcgsc.ca	37	19	7986374	7986374	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SNAPC2	NM_003083	exon2	c.G250A	p.G84S	.	.	93	4	81	0	.	90
SNX18	112574	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	53815183	53815183	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SNX18	NM_052870	exon1	c.G1401A	p.V467V	.	.	60	19	85	1	.	226
SOX14	8403	hgsc.bcm.edu;bcgsc.ca	37	3	137483875	137483875	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SOX14	NM_004189	exon1	c.C249G	p.P83P	.	.	131	9	159	0	.	90
SPAG5	10615	bcgsc.ca	37	17	26910958	26910958	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPAG5	NM_006461	exon14	c.T2459C	p.V820A	.	.	150	7	126	0	.	90
SPAG6	9576	bcgsc.ca	37	10	22700080	22700080	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPAG6	NM_012443	exon10	c.A1435G	p.S479G	.	.	79	4	101	0	.	153
SPAG9	9043	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	49075937	49075937	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPAG9	NM_001130528	exon15	c.A1706C	p.K569T	.	.	386	47	288	0	.	659
SPATA2L	124044	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	89764069	89764069	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPATA2L	NM_152339	exon3	c.G948C	p.L316L	.	.	91	18	65	0	.	90
SPATA31C1	441452	bcgsc.ca;mdanderson.org	37	9	90536519	90536519	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145124	exon4	c.G1697A	p.G566E	.	.	114	25	164	1	.	.
SPATA31E1	286234	bcgsc.ca	37	9	90497916	90497916	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_178828	exon1	c.A110G	p.D37G	.	.	135	5	182	1	.	.
SPATA8	145946	bcgsc.ca	37	15	97327407	97327407	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPATA8	NM_173499	exon2	c.A114G	p.E38E	.	.	80	3	109	0	.	92
SPDYE3	441272	broad.mit.edu	37	7	99917393	99917393	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPDYE3	NM_001004351	exon9	c.C1552A	p.R518S	.	.	158	8	197	1	.	22
SPEF2	79925	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	35807028	35807028	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPEF2	NM_024867	exon35	c.C5230A	p.L1744I	.	.	325	116	369	0	.	26
SPOCD1	90853	bcgsc.ca	37	1	32258004	32258004	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPOCD1	NM_144569	exon16	c.2776-2A>G	.	.	.	118	5	188	0	.	158
SPTB	6710	bcgsc.ca	37	14	65253668	65253668	+	Silent	SNP	G	G	A	rs147235045	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPTB	NM_001024858	exon15	c.C3015T	p.A1005A	.	.	60	13	50	1	G|0.999;A|0.001	100
SPTBN1	6711	bcgsc.ca	37	2	54873063	54873063	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPTBN1	NM_003128	exon22	c.4495-2A>G	.	.	.	70	4	66	0	.	140
SPTLC2	9517	bcgsc.ca	37	14	78018469	78018469	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPTLC2	NM_004863	exon9	c.T1273C	p.C425R	.	.	103	6	126	0	.	92
SPTY2D1	144108	hgsc.bcm.edu	37	11	18637172	18637173	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPTY2D1	NM_194285	exon3	c.649_650insA	p.L217fs	.	.	253	17	294	0	.	90
SPZ1	84654	hgsc.bcm.edu	37	5	79616680	79616681	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SPZ1	NM_032567	exon1	c.646_647insA	p.E216fs	.	.	256	18	194	0	.	91
SRCRB4D	136853	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	76029631	76029631	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SRCRB4D	NM_080744	exon4	c.C447G	p.H149Q	.	.	147	51	184	0	.	91
SRL	6345	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	4242512	4242512	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SRL	NM_001098814	exon6	c.A1064T	p.K355M	.	.	263	43	233	0	.	73
SSTR3	6753	hgsc.bcm.edu;bcgsc.ca	37	22	37602710	37602710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SSTR3	NM_001051	exon2	c.C1133T	p.T378M	.	.	82	5	104	0	.	522
ST18	9705	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	53092714	53092714	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ST18	NM_014682	exon9	c.G245T	p.G82V	.	.	260	47	354	0	.	95
ST8SIA6	338596	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	17365101	17365101	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ST8SIA6	NM_001004470	exon7	c.A691T	p.N231Y	.	.	266	62	354	0	.	91
STAT3	6774	bcgsc.ca	37	17	40475631	40475631	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STAT3	NM_003150	exon18	c.A1613G	p.N538S	.	.	160	5	126	0	.	1271
STK31	56164	hgsc.bcm.edu;broad.mit.edu	37	7	23775340	23775341	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STK31	NM_001260505	exon7	c.667_668insA	p.E223fs	.	.	141	12	121	0	.	338
STON1-GTF2A1L	286749	hgsc.bcm.edu;broad.mit.edu	37	2	48809580	48809581	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STON1-GTF2A1L	NM_001198593	exon2	c.1808_1809insG	p.L603fs	.	.	164	11	151	0	.	27
STOX2	56977	broad.mit.edu;bcgsc.ca	37	4	184931964	184931965	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	STOX2	NM_020225	exon3	c.1973_1974insA	p.P658fs	.	.	74	9	68	0	.	22
STPG2	285555	bcgsc.ca	37	4	99027180	99027180	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_174952	exon5	c.A536G	p.K179R	.	.	193	6	201	0	.	.
SUPT6H	6830	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	27001353	27001353	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SUPT6H	NM_003170	exon3	c.G162T	p.L54F	.	.	284	31	192	0	.	93
SVEP1	79987	bcgsc.ca	37	9	113191496	113191496	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SVEP1	NM_153366	exon35	c.A5734G	p.N1912D	.	.	82	4	94	0	.	75
SVOPL	136306	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	138312995	138312996	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SVOPL	NM_001139456	exon10	c.977_978insG	p.D326fs	.	.	131	13	139	0	.	68
SWAP70	23075	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	9769515	9769515	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	SWAP70	NM_015055	exon10	c.G1466A	p.R489H	.	.	96	17	125	0	.	228
SYNE4	163183	hgsc.bcm.edu;ucsc.edu;mdanderson.org	37	19	36496296	36496296	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001039876	exon6	c.G911A	p.G304D	.	.	197	32	172	0	.	.
TADA2A	6871	bcgsc.ca	37	17	35802704	35802704	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TADA2A	NM_001488	exon7	c.T482C	p.L161P	.	.	210	6	157	0	.	230
TAF7L	54457	hgsc.bcm.edu	37	X	100531419	100531419	+	Silent	SNP	C	C	T	rs147505183	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TAF7L	NM_024885	exon10	c.G1047A	p.E349E	.	.	151	36	148	0	C|0.997;T|0.003	130
TAF7L	54457	hgsc.bcm.edu	37	X	100531437	100531437	+	Silent	SNP	C	C	T	rs148266047	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TAF7L	NM_024885	exon10	c.G1029A	p.E343E	.	.	150	33	151	0	C|0.996;T|0.004	130
TBC1D1	23216	bcgsc.ca	37	4	38126642	38126642	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TBC1D1	NM_015173	exon18	c.A3022G	p.S1008G	.	.	201	7	209	2	.	91
TBCE	6905	bcgsc.ca	37	1	235599706	235599706	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TBCE	NM_003193	exon10	c.A839G	p.E280G	.	.	149	5	129	0	.	90
TCEB3CL2	100506888	broad.mit.edu;bcgsc.ca	37	18	44543597	44543598	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001242907	exon1	c.775_776insG	p.P259fs	.	.	217	14	250	0	.	.
TCF4	6925	bcgsc.ca	37	18	53128290	53128290	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TCF4	NM_001243226	exon6	c.T570C	p.H190H	.	.	118	5	115	1	.	523
TCF7L1	83439	broad.mit.edu;bcgsc.ca	37	2	85536234	85536235	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TCF7L1	NM_031283	exon12	c.1416_1417insG	p.H472fs	.	.	78	8	109	0	.	585
TCL6	27004	broad.mit.edu	37	14	96135797	96135797	+	RNA	SNP	A	A	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TCL6	.	.	.	.	.	.	17	10	36	0	.	658
TCP10	6953	hgsc.bcm.edu	37	6	167790069	167790070	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TCP10	NM_004610	exon5	c.541_542insC	p.G181fs	.	.	336	26	294	0	.	89
TDGF1P3	6998	bcgsc.ca	37	X	109764719	109764719	+	RNA	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	87	5	104	0	.	.
TENM1	10178	bcgsc.ca	37	X	124029882	124029882	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001163278	exon2	c.T426C	p.S142S	.	.	139	5	150	0	.	.
TERF1	7013	hgsc.bcm.edu;broad.mit.edu	37	8	73951354	73951355	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TERF1	NM_017489	exon9	c.1043_1044insA	p.T348fs	.	.	135	11	102	0	.	228
TEX10	54881	bcgsc.ca	37	9	103083979	103083979	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TEX10	NM_001161584	exon10	c.T2063C	p.F688S	.	.	45	4	52	0	.	92
THRAP3	9967	hgsc.bcm.edu;broad.mit.edu	37	1	36755000	36755001	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	THRAP3	NM_005119	exon5	c.1380_1381insA	p.N460fs	.	.	128	10	126	0	.	663
THRB	7068	hgsc.bcm.edu	37	3	24164402	24164403	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	THRB	NM_000461	exon10	c.1359_1360insC	p.P453fs	.	.	119	10	162	0	.	227
TMED9	54732	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	177019352	177019354	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMED9	NM_017510	exon1	c.137_139del	p.46_47del	.	.	250	0	285	0	.	90
TMEM125	128218	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	43738869	43738869	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMEM125	NM_144626	exon4	c.C476T	p.S159L	.	.	378	84	416	2	.	153
TMEM186	25880	hgsc.bcm.edu;bcgsc.ca	37	16	8890210	8890210	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMEM186	NM_015421	exon2	c.C241G	p.L81V	.	.	123	8	129	0	.	91
TMEM208	29100	bcgsc.ca	37	16	67261762	67261762	+	Silent	SNP	A	A	G	rs9941017		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_014187	exon2	c.A30G	p.R10R	.	.	75	4	90	0	A|1.000;|0.000	.
TMEM5	10329	bcgsc.ca	37	12	64202846	64202846	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMEM5	NM_014254	exon6	c.T1306C	p.S436P	.	.	53	4	33	0	.	90
TMOD3	29766	bcgsc.ca	37	15	52155194	52155194	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMOD3	NM_014547	exon2	c.A113G	p.D38G	.	.	181	6	235	0	.	91
TMPRSS4	56649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	117979580	117979580	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TMPRSS4	NM_019894	exon7	c.C552T	p.L184L	.	.	76	40	107	0	.	90
TPP1	1200	bcgsc.ca	37	11	6636719	6636719	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TPP1	NM_000391	exon10	c.T1220C	p.I407T	.	.	150	5	182	0	.	90
TPRX1	284355	hgsc.bcm.edu;broad.mit.edu	37	19	48305271	48305272	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TPRX1	NM_198479	exon2	c.997_998insC	p.L333fs	.	.	160	11	122	0	.	90
TRABD2A	129293	bcgsc.ca	37	2	85097710	85097710	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001080824	exon2	c.A308G	p.Q103R	.	.	81	5	108	1	.	.
TRAF3IP3	80342	bcgsc.ca	37	1	209953848	209953848	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRAF3IP3	NM_025228	exon15	c.T1346C	p.F449S	.	.	172	7	149	1	.	291
TRANK1	9881	broad.mit.edu;bcgsc.ca	37	3	36899168	36899169	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRANK1	NM_014831	exon12	c.1913_1914insC	p.Q638fs	.	.	60	7	115	0	.	24
TRIM13	10206	hgsc.bcm.edu	37	13	50591338	50591339	+	RNA	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRIM13	.	.	.	.	.	.	145	15	138	0	.	228
TRIM29	23650	bcgsc.ca	37	11	119996417	119996417	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRIM29	NM_012101	exon4	c.A1315G	p.R439G	.	.	148	5	229	0	.	291
TRIOBP	11078	bcgsc.ca	37	22	38120006	38120006	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRIOBP	NM_001039141	exon7	c.T1443C	p.C481C	.	.	357	27	395	12	.	136
TRIOBP	11078	broad.mit.edu;bcgsc.ca	37	22	38130525	38130526	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRIOBP	NM_001039141	exon9	c.4182_4183insC	p.L1394fs	.	.	99	10	85	0	.	136
TRPV1	7442	bcgsc.ca	37	17	3489100	3489100	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TRPV1	NM_018727	exon8	c.T1345C	p.F449L	.	.	74	5	120	0	.	23
TSHR	7253	hgsc.bcm.edu;broad.mit.edu	37	14	81609512	81609513	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TSHR	NM_000369	exon10	c.1110_1111insA	p.L370fs	.	.	188	12	213	0	.	1650
TTC1	7265	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	159437629	159437629	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTC1	NM_003314	exon2	c.C94G	p.P32A	.	.	97	38	87	0	.	91
TTC27	55622	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	33012108	33012108	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTC27	NM_017735	exon16	c.G1890T	p.Q630H	.	.	153	23	187	0	.	90
TTC40	54777	hgsc.bcm.edu;broad.mit.edu	37	10	134726617	134726618	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001200049	exon18	c.2266_2267insG	p.R756fs	.	.	126	10	166	0	.	.
TTC9	23508	bcgsc.ca	37	14	71134368	71134368	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_015351	exon2	c.A494G	p.K165R	.	.	111	5	165	1	.	.
TTF1	7270	hgsc.bcm.edu	37	9	135277201	135277202	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTF1	NM_007344	exon2	c.1008_1009insA	p.K336fs	.	.	151	0	164	0	.	94
TTLL4	9654	bcgsc.ca	37	2	219618335	219618335	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTLL4	NM_014640	exon19	c.T3287C	p.I1096T	.	.	130	6	140	0	.	93
TTN	7273	bcgsc.ca	37	2	179442828	179442828	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTN	NM_001267550	exon322	c.T68414C	p.V22805A	.	.	145	5	141	0	.	636
TTN	7273	broad.mit.edu;bcgsc.ca	37	2	179511798	179511799	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TTN	NM_001267550	exon215	c.40215_40216insC	p.P13405fs	.	.	162	18	138	0	.	636
TUBA3C	7278	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	19751669	19751669	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	TUBA3C	NM_006001	exon4	c.C454G	p.L152V	.	.	358	78	570	0	.	95
TVP23C	201158	bcgsc.ca	37	17	15443864	15443864	+	Silent	SNP	A	A	G	rs2589694		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001135036	exon6	c.T474C	p.I158I	.	.	480	22	721	1	.	.
UBR7	55148	bcgsc.ca	37	14	93678428	93678428	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UBR7	NM_175748	exon4	c.A396G	p.G132G	.	.	86	6	90	0	.	90
UMODL1	89766	broad.mit.edu;mdanderson.org	37	21	43529800	43529800	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UMODL1	NM_173568	exon10	c.G1648A	p.A550T	.	.	17	7	15	0	.	93
UNKL	64718	hgsc.bcm.edu;broad.mit.edu	37	16	1417771	1417772	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UNKL	NM_001193388	exon13	c.1674_1675insC	p.P558fs	.	.	185	11	196	0	.	90
USP31	57478	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	23093878	23093878	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	USP31	NM_020718	exon12	c.C1831G	p.L611V	.	.	168	30	133	0	.	663
USP32P2	220594	broad.mit.edu	37	17	18422997	18422997	+	RNA	SNP	G	G	A	rs1725636		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	105	7	128	0	.	.
USP32P2	220594	bcgsc.ca	37	17	18422839	18422839	+	RNA	SNP	A	A	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	239	12	249	2	.	.
USP36	57602	hgsc.bcm.edu	37	17	76798561	76798561	+	Missense_Mutation	SNP	T	T	C	rs75975389	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	USP36	NM_025090	exon17	c.A2867G	p.K956R	.	.	109	9	88	0	T|0.994;C|0.006	659
UTP20	27340	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	101711355	101711355	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	UTP20	NM_014503	exon22	c.C2652T	p.A884A	.	.	141	32	138	0	.	155
VCX2	51480	broad.mit.edu	37	X	8138220	8138220	+	Silent	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VCX2	NM_016378	exon3	c.G273C	p.P91P	.	.	27	15	22	0	.	22
VCX	26609	hgsc.bcm.edu;bcgsc.ca	37	X	7811709	7811709	+	Silent	SNP	G	G	C	rs139507263	byfrequency;alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VCX	NM_013452	exon3	c.G273C	p.P91P	.	.	84	28	81	0	G|0.999;A|0.001	22
VN1R4	317703	bcgsc.ca	37	19	53770569	53770569	+	Missense_Mutation	SNP	G	G	C	rs74359534		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VN1R4	NM_173857	exon1	c.C350G	p.A117G	.	.	383	11	381	0	G|0.500;C|0.500	92
VWDE	221806	ucsc.edu;bcgsc.ca;mdanderson.org	37	7	12397021	12397021	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	VWDE	NM_001135924	exon17	c.A3395G	p.D1132G	.	.	151	43	142	1	.	68
WARS	7453	hgsc.bcm.edu	37	14	100808872	100808873	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WARS	NM_004184	exon9	c.976_977insC	p.R326fs	.	.	208	15	249	0	.	153
WDR44	54521	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	117528110	117528110	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDR44	NM_001184965	exon5	c.G919T	p.A307S	.	.	148	105	190	0	.	133
WDR73	84942	hgsc.bcm.edu	37	15	85186892	85186892	+	Missense_Mutation	SNP	C	C	T	rs199676984		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDR73	NM_032856	exon8	c.G946A	p.G316R	.	.	115	10	139	0	.	90
WDR73	84942	hgsc.bcm.edu	37	15	85186894	85186894	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDR73	NM_032856	exon8	c.944delA	p.D315fs	.	.	114	10	135	0	.	90
WDR92	116143	bcgsc.ca	37	2	68365973	68365973	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDR92	NM_001256476	exon5	c.A534G	p.Q178Q	.	.	211	6	180	0	.	68
WDTC1	23038	hgsc.bcm.edu;broad.mit.edu	37	1	27622887	27622888	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WDTC1	NM_015023	exon10	c.944_945insG	p.S315fs	.	.	237	17	415	0	.	91
WNT6	7475	broad.mit.edu;bcgsc.ca	37	2	219735805	219735814	+	Frame_Shift_Del	DEL	GGCTGGCCGG	GGCTGGCCGG	-	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	GGCTGGCCGG	GGCTGGCCGG	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	WNT6	NM_006522	exon2	c.137_146del	p.46_49del	.	.	61	7	73	0	.	564
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu	37	2	168104502	168104503	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	XIRP2	NM_152381	exon9	c.6600_6601insA	p.K2200fs	.	.	172	11	153	0	.	104
XPC	7508	bcgsc.ca	37	3	14200013	14200013	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	XPC	NM_004628	exon9	c.A1370G	p.D457G	.	.	59	4	75	1	.	662
XPO4	64328	ucsc.edu;bcgsc.ca;mdanderson.org	37	13	21418016	21418016	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	XPO4	NM_022459	exon5	c.G466C	p.A156P	.	.	62	11	79	0	.	272
YARS2	51067	bcgsc.ca	37	12	32900280	32900280	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	YARS2	NM_001040436	exon5	c.A1292G	p.E431G	.	.	201	6	205	0	.	90
YIPF3	25844	bcgsc.ca	37	6	43483344	43483344	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	YIPF3	NM_015388	exon3	c.G384T	p.Q128H	.	.	90	4	118	1	.	90
ZBTB39	9880	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	57397205	57397205	+	Silent	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZBTB39	NM_014830	exon2	c.G1497A	p.T499T	.	.	63	14	63	0	.	135
ZBTB49	166793	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	4303971	4303971	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZBTB49	NM_145291	exon3	c.A408G	p.L136L	.	.	98	48	114	0	.	92
ZBTB8B	728116	bcgsc.ca	37	1	32946615	32946615	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001145720	exon3	c.A1115G	p.E372G	.	.	44	4	118	1	.	.
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937856	88937856	+	Missense_Mutation	SNP	T	T	C	rs75851694	byfrequency	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZCCHC6	NM_024617	exon13	c.A2809G	p.K937E	.	.	326	20	494	0	T|0.980;C|0.020	92
ZDHHC21	340481	bcgsc.ca	37	9	14619018	14619018	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZDHHC21	NM_178566	exon10	c.T744C	p.P248P	.	.	99	5	150	1	.	226
ZEB2	9839	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	145187479	145187479	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZEB2	NM_001171653	exon3	c.C188G	p.A63G	.	.	252	97	282	0	.	297
ZFYVE16	9765	ucsc.edu;mdanderson.org	37	5	79739077	79739077	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZFYVE16	NM_001105251	exon6	c.C2555G	p.S852X	.	.	418	51	352	1	.	90
ZFYVE20	64145	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	15126258	15126258	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZFYVE20	NM_022340	exon8	c.C582T	p.I194I	.	.	125	65	142	0	.	92
ZNF143	7702	bcgsc.ca	37	11	9501020	9501020	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF143	NM_003442	exon7	c.T572C	p.V191A	.	.	90	4	98	0	.	90
ZNF20	7568	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	12243428	12243428	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF20	NM_021143	exon4	c.G1573C	p.E525Q	.	.	192	64	145	0	.	22
ZNF217	7764	hgsc.bcm.edu	37	20	52199201	52199202	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF217	NM_006526	exon1	c.165_166insA	p.N55fs	.	.	155	10	151	0	.	723
ZNF224	7767	bcgsc.ca	37	19	44611786	44611786	+	Silent	SNP	G	G	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF224	NM_013398	exon6	c.G1473A	p.K491K	.	.	172	7	171	1	.	92
ZNF334	55713	bcgsc.ca	37	20	45131039	45131039	+	Silent	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF334	NM_018102	exon5	c.A939G	p.K313K	.	.	127	5	121	0	.	92
ZNF462	58499	bcgsc.ca	37	9	109691562	109691562	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF462	NM_021224	exon3	c.A5369G	p.H1790R	.	.	85	4	119	0	.	95
ZNF521	25925	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	22804595	22804595	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF521	NM_015461	exon4	c.G3287A	p.C1096Y	.	.	104	75	135	0	.	275
ZNF587B	100293516	broad.mit.edu;bcgsc.ca	37	19	58352303	58352304	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001204818	exon3	c.261_262insC	p.S87fs	.	.	313	8	294	0	.	.
ZNF641	121274	bcgsc.ca	37	12	48737512	48737512	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF641	NM_001172681	exon7	c.521-2A>G	.	.	.	86	4	82	0	.	92
ZNF658	26149	broad.mit.edu;bcgsc.ca	37	9	40772354	40772355	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	-	-	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF658	NM_033160	exon5	c.2921_2922insA	p.T974fs	.	.	440	9	594	0	.	45
ZNF675	171392	hgsc.bcm.edu	37	19	23836432	23836432	+	Nonsense_Mutation	SNP	G	G	A	rs199957959		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF675	NM_138330	exon4	c.C1303T	p.R435X	.	.	70	6	82	0	G|0.999;A|0.001	228
ZNF695	57116	ucsc.edu;bcgsc.ca	37	1	247150812	247150812	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_020394	exon4	c.G1005T	p.L335F	.	.	110	11	105	9	.	.
ZNF701	55762	bcgsc.ca	37	19	53085660	53085660	+	Silent	SNP	C	C	A	rs140636201	byfrequency;alternate_allele	TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF701	NM_001172655	exon5	c.C546A	p.T182T	.	.	455	13	529	1	C|0.998;T|0.002	90
ZNF714	148206	hgsc.bcm.edu	37	19	21299774	21299774	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF714	NM_182515	exon5	c.T304A	p.Y102N	.	.	278	0	286	0	.	67
ZNF737	100129842	bcgsc.ca	37	19	20728306	20728306	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF737	NM_001159293	exon4	c.G703A	p.G235S	.	.	123	5	88	0	.	1
ZNF814	730051	ucsc.edu	37	19	58384418	58384418	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	NM_001144989	exon3	c.T2340C	p.S780S	.	.	174	1	180	0	.	.
ZNF833P	401898	bcgsc.ca	37	19	11794982	11794982	+	RNA	SNP	T	T	C	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZNF833P	.	.	.	.	.	.	41	4	37	0	.	91
ZP4	57829	hgsc.bcm.edu;bcgsc.ca	37	1	238053180	238053180	+	Silent	SNP	A	A	G	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	ZP4	NM_021186	exon3	c.T387C	p.P129P	.	.	174	40	141	0	.	93
OR11H12	440153	bcgsc.ca	37	14	19807080	19807081	+	RNA	DNP	CA	CA	AC	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CA	CA	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	.	.	.	.	.	
OR11H12	440153	bcgsc.ca	37	14	19807082	19807083	+	RNA	DNP	AT	AT	TC	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	AT	AT	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	.	.	.	.	.	
RTTN	25914	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	18	67794863	67794864	+	Missense_Mutation	DNP	CC	CC	AA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	p.R1086I	.	.	.	.	.	.	.	
NPSR1	387129	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	7	34888201	34888202	+	Missense_Mutation	DNP	CC	CC	AA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	p.NL317KM	.	.	.	.	.	.	.	
RP11-561N12.5	0	bcgsc.ca	37	7	64030018	64030019	+	RNA	DNP	CC	CC	AA	novel		TCGA-BC-A112-01A-11D-A12Z-10	TCGA-BC-A112-11A-11D-A12Z-10	CC	CC	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b3d19f75-db62-42cc-8a6f-7685ab1f3b9b	bb1973b9-7ab8-4bbc-beb1-9448f91ad7ef	.	.	.	.	.	.	.	.	.	.	.	.	.	
