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
A2M	2	ucsc.edu;bcgsc.ca	37	12	9241795	9241795	+	Splice_Site	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	A2M	NM_000014	exon23	c.2770+1G>T	.	.	.	117	47	121	1	.	515
ABCC6P1	653190	ucsc.edu;bcgsc.ca	37	16	18591534	18591534	+	RNA	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	201	74	267	0	.	.
ABLIM1	3983	bcgsc.ca	37	10	116201493	116201493	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ABLIM1	NM_002313	exon18	c.T1986C	p.N662N	.	.	75	3	123	0	.	153
ACAN	176	hgsc.bcm.edu;broad.mit.edu	37	15	89415310	89415310	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ACAN	NM_013227	exon15	c.7182delC	p.H2394fs	.	.	147	10	170	0	.	25
ACSBG2	81616	bcgsc.ca	37	19	6161259	6161259	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ACSBG2	NM_030924	exon6	c.A541G	p.I181V	.	.	88	4	93	0	.	23
ACSS1	84532	hgsc.bcm.edu;broad.mit.edu	37	20	25002140	25002140	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ACSS1	NM_001252677	exon6	c.993delT	p.F331fs	.	.	168	10	177	0	.	92
ADCK1	57143	bcgsc.ca	37	14	78325534	78325534	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ADCK1	NM_020421	exon4	c.335delC	p.T112fs	.	.	40	4	75	0	.	334
ADCK5	203054	bcgsc.ca	37	8	145616809	145616809	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ADCK5	NM_174922	exon8	c.828delG	p.L276fs	.	.	36	5	85	0	.	333
ADRB3	155	bcgsc.ca	37	8	37823798	37823798	+	Missense_Mutation	SNP	A	A	G	rs4994	bycluster;byfrequency;by1000genomes	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ADRB3	NM_000025	exon1	c.T190C	p.W64R	.	.	88	4	143	0	A|0.906;G|0.094	522
AFAP1	60312	bcgsc.ca	37	4	7870388	7870388	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AFAP1	NM_001134647	exon3	c.T186C	p.P62P	.	.	52	4	54	1	.	90
AGPAT2	10555	bcgsc.ca	37	9	139569213	139569213	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AGPAT2	NM_006412	exon5	c.A635G	p.N212S	.	.	53	4	64	0	.	90
AGPAT5	55326	bcgsc.ca	37	8	6599206	6599206	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AGPAT5	NM_018361	exon5	c.520delG	p.G174fs	.	.	43	4	80	0	.	90
AHNAK2	113146	bcgsc.ca	37	14	105407171	105407171	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AHNAK2	NM_138420	exon7	c.14617delT	p.S4873fs	.	.	30	4	81	0	.	47
AK7	122481	bcgsc.ca	37	14	96924422	96924422	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AK7	NM_152327	exon12	c.1230delG	p.E410fs	.	.	28	3	95	0	.	228
ALDH1A3	220	bcgsc.ca	37	15	101425535	101425535	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ALDH1A3	NM_000693	exon2	c.T163C	p.S55P	.	.	84	4	88	0	.	651
ALOX12	239	bcgsc.ca	37	17	6909195	6909195	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ALOX12	NM_000697	exon10	c.1267delG	p.G423fs	.	.	41	5	61	0	.	226
ANK3	288	bcgsc.ca	37	10	61822911	61822911	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ANK3	NM_020987	exon40	c.A12553G	p.S4185G	.	.	90	5	88	0	.	107
ANKRD10	55608	bcgsc.ca	37	13	111532117	111532117	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ANKRD10	NM_017664	exon6	c.A1130G	p.Y377C	.	.	77	4	80	0	.	226
ANKRD13A	88455	bcgsc.ca	37	12	110468463	110468463	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ANKRD13A	NM_033121	exon12	c.T1248C	p.F416F	.	.	29	4	53	0	.	90
ANKS1A	23294	bcgsc.ca	37	6	34949608	34949608	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ANKS1A	NM_015245	exon4	c.G577T	p.G193W	.	.	381	9	206	2	.	94
ANXA3	306	bcgsc.ca	37	4	79512700	79512700	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ANXA3	NM_005139	exon7	c.T406C	p.Y136H	.	.	84	4	101	0	.	90
AP3B2	8120	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	83331627	83331627	+	Silent	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AP3B2	NM_004644	exon22	c.G2595T	p.R865R	.	.	72	43	62	0	.	94
AP4E1	23431	bcgsc.ca	37	15	51291314	51291314	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	AP4E1	NM_007347	exon19	c.A2950G	p.S984G	.	.	197	6	163	0	.	90
ARFGEF1	10565	bcgsc.ca	37	8	68139385	68139385	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ARFGEF1	NM_006421	exon27	c.3903delC	p.T1301fs	.	.	49	5	87	0	.	294
ARHGEF17	9828	hgsc.bcm.edu;broad.mit.edu	37	11	73020687	73020687	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ARHGEF17	NM_014786	exon1	c.1004delC	p.A335fs	.	.	133	10	98	0	.	227
ARID1B	57492	hgsc.bcm.edu;broad.mit.edu	37	6	157528676	157528676	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ARID1B	NM_020732	exon20	c.6401delT	p.L2134fs	.	.	154	10	123	0	.	154
ARL16	339231	bcgsc.ca	37	17	79649135	79649135	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001040025	exon4	c.T351C	p.C117C	.	.	219	8	208	0	.	.
ARMC1	55156	ucsc.edu;bcgsc.ca;mdanderson.org	37	8	66525548	66525548	+	Silent	SNP	T	T	C	rs11559265	byfrequency	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ARMC1	NM_018120	exon4	c.A396G	p.Q132Q	.	.	103	90	228	0	T|0.731;C|0.269	91
ARMC6	93436	bcgsc.ca	37	19	19162464	19162464	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ARMC6	NM_001199196	exon5	c.T313C	p.S105P	.	.	60	4	144	0	.	90
ASB15	142685	bcgsc.ca	37	7	123257789	123257789	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ASB15	NM_080928	exon5	c.449delT	p.I150fs	.	.	36	4	68	0	.	228
ATP10D	57205	bcgsc.ca	37	4	47559792	47559792	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ATP10D	NM_020453	exon12	c.A1936G	p.K646E	.	.	72	4	83	0	.	93
ATP13A2	23400	bcgsc.ca	37	1	17322949	17322949	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ATP13A2	NM_022089	exon13	c.A1238G	p.H413R	.	.	203	7	255	3	.	93
BAZ1B	9031	bcgsc.ca	37	7	72873947	72873947	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	BAZ1B	NM_032408	exon13	c.A3351G	p.Q1117Q	.	.	102	4	195	1	.	159
BAZ2B	29994	bcgsc.ca	37	2	160181459	160181459	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	BAZ2B	NM_013450	exon36	c.T6216C	p.I2072I	.	.	206	6	207	0	.	94
BRCA1	672	bcgsc.ca	37	17	41276097	41276097	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	BRCA1	NM_007298	exon1	c.T17C	p.L6P	.	.	101	3	169	0	.	3415
C10orf107	219621	hgsc.bcm.edu;broad.mit.edu	37	10	63441027	63441027	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	C10orf107	NM_173554	exon2	c.27delA	p.S9fs	.	.	104	10	75	0	.	90
C15orf43	145645	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	15	45250636	45250636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	C15orf43	NM_152448	exon3	c.C212T	p.A71V	.	.	142	72	119	0	.	90
C17orf53	78995	bcgsc.ca	37	17	42228343	42228343	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	C17orf53	NM_001171251	exon4	c.T1239C	p.S413S	.	.	117	5	227	0	.	90
C20orf26	26074	bcgsc.ca	37	20	20037373	20037373	+	Missense_Mutation	SNP	T	T	C	rs142975667		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	C20orf26	NM_015585	exon2	c.T76C	p.C26R	.	.	146	5	161	0	T|1.000;C|0.000	94
C7orf55-LUC7L2	100996928	bcgsc.ca	37	7	139086965	139086965	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001244584	exon5	c.536delA	p.E179fs	.	.	40	4	64	0	.	.
C9orf72	203228	hgsc.bcm.edu;broad.mit.edu	37	9	27566850	27566850	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	C9orf72	NM_018325	exon2	c.269delA	p.K90fs	.	.	180	13	184	0	.	517
CAB39L	81617	bcgsc.ca	37	13	49951194	49951194	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CAB39L	NM_030925	exon3	c.C185G	p.P62R	.	.	173	6	231	2	.	90
CACNA1B	774	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	9	140878654	140878654	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CACNA1B	NM_001243812	exon13	c.T1721A	p.I574N	.	.	234	102	283	1	.	138
CACNA1E	777	bcgsc.ca	37	1	181759658	181759658	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CACNA1E	NM_001205293	exon44	c.C5864A	p.A1955D	.	.	493	12	177	2	.	95
CACNA1E	777	hgsc.bcm.edu	37	1	181701550	181701550	+	Silent	SNP	C	C	T	rs182071786	by1000genomes	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CACNA1E	NM_001205293	exon20	c.C2328T	p.S776S	.	.	375	41	221	0	C|0.996;T|0.004	95
CADPS	8618	ucsc.edu;bcgsc.ca;mdanderson.org	37	3	62502268	62502268	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CADPS	NM_003716	exon15	c.C2444T	p.S815L	.	.	266	91	271	0	.	281
CAPN12	147968	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	39226821	39226821	+	Silent	SNP	C	C	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CAPN12	NM_144691	exon12	c.G1512C	p.P504P	.	.	31	15	55	0	.	91
CAPZA2	830	bcgsc.ca	37	7	116557794	116557794	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CAPZA2	NM_006136	exon10	c.A734G	p.E245G	.	.	94	4	162	0	.	514
CARM1	10498	bcgsc.ca	37	19	11019798	11019798	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CARM1	NM_199141	exon4	c.A473G	p.Q158R	.	.	64	4	92	0	.	90
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CCDC102A	NM_033212	exon2	c.C286T	p.R96W	.	.	10	10	0	0	G|0.001;A|0.999	91
CCDC144C	348254	bcgsc.ca	37	17	20297499	20297499	+	RNA	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	122	8	155	2	.	.
CCDC171	203238	bcgsc.ca	37	9	15777602	15777602	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_173550	exon19	c.A2676G	p.P892P	.	.	38	4	57	0	.	.
CCDC88A	55704	bcgsc.ca	37	2	55543065	55543065	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CCDC88A	NM_018084	exon22	c.A3932G	p.E1311G	.	.	83	4	164	0	.	94
CDC123	8872	hgsc.bcm.edu;bcgsc.ca	37	10	12259467	12259470	+	Splice_Site	DEL	GTAA	GTAA	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CDC123	.	.	.	.	.	.	75	0	108	0	.	514
CEL	1056	hgsc.bcm.edu;bcgsc.ca	37	9	135944115	135944115	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CEL	NM_001807	exon8	c.G961T	p.A321S	.	.	650	122	834	1	.	91
CELSR3	1951	bcgsc.ca	37	3	48683186	48683186	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CELSR3	NM_001407	exon23	c.T7579C	p.S2527P	.	.	88	4	76	1	.	523
CENPT	80152	bcgsc.ca	37	16	67863958	67863958	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CENPT	NM_025082	exon12	c.A896G	p.E299G	.	.	59	4	109	0	.	90
CEP170B	283638	bcgsc.ca	37	14	105352395	105352395	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001112726	exon11	c.T1963C	p.S655P	.	.	63	4	84	0	.	.
CIAPIN1	57019	bcgsc.ca	37	16	57467977	57467977	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CIAPIN1	NM_020313	exon5	c.A535G	p.T179A	.	.	73	4	135	1	.	90
CKAP5	9793	ucsc.edu;bcgsc.ca	37	11	46829629	46829629	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CKAP5	NM_001008938	exon8	c.C930T	p.P310P	.	.	225	97	199	1	.	92
CLASRP	11129	bcgsc.ca	37	19	45556144	45556144	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CLASRP	NM_007056	exon4	c.293delC	p.T98fs	.	.	47	5	74	0	.	154
CNKSR1	10256	bcgsc.ca	37	1	26507297	26507297	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CNKSR1	NM_006314	exon3	c.T302C	p.L101P	.	.	253	7	287	0	.	846
CNTN6	27255	bcgsc.ca	37	3	1414137	1414137	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CNTN6	NM_014461	exon13	c.T1647C	p.A549A	.	.	48	4	66	0	.	345
COL11A1	1301	bcgsc.ca	37	1	103400098	103400098	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	COL11A1	NM_080629	exon46	c.A3543G	p.E1181E	.	.	142	5	163	0	.	586
COL22A1	169044	bcgsc.ca	37	8	139675977	139675977	+	Frame_Shift_Del	DEL	A	A	-	rs5895546		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	COL22A1	NM_152888	exon42	c.3157delT	p.S1053fs	.	.	31	3	75	0	.	103
COL22A1	169044	bcgsc.ca	37	8	139712381	139712381	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	COL22A1	NM_152888	exon32	c.2566delC	p.L856fs	.	.	39	4	78	0	.	103
COL6A1	1291	bcgsc.ca	37	21	47421253	47421253	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	COL6A1	NM_001848	exon30	c.T1909C	p.F637L	.	.	44	4	56	0	.	91
COL6A6	131873	ucsc.edu;bcgsc.ca	37	3	130282159	130282159	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	COL6A6	NM_001102608	exon2	c.C312T	p.S104S	.	.	172	82	198	1	.	76
CPEB2	132864	bcgsc.ca	37	4	15060074	15060074	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CPEB2	NM_001177382	exon9	c.A2491G	p.S831G	.	.	129	5	127	0	.	91
CPT1A	1374	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	68530124	68530124	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CPT1A	NM_001876	exon15	c.G1846A	p.V616M	.	.	85	34	81	0	.	149
CRISPLD1	83690	bcgsc.ca	37	8	75929308	75929308	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CRISPLD1	NM_031461	exon9	c.A956G	p.D319G	.	.	45	4	102	0	.	91
CSMD1	64478	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	3216824	3216824	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CSMD1	NM_033225	exon21	c.G3154T	p.A1052S	.	.	86	71	151	0	.	86
CSMD3	114788	bcgsc.ca	37	8	113364738	113364738	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CSMD3	NM_198123	exon39	c.A6162G	p.E2054E	.	.	86	4	168	0	.	1132
CSPP1	79848	bcgsc.ca	37	8	68007674	68007674	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CSPP1	NM_024790	exon6	c.A657G	p.R219R	.	.	60	4	98	0	.	138
CTSA	5476	bcgsc.ca	37	20	44520305	44520305	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CTSA	NM_000308	exon2	c.A152G	p.D51G	.	.	103	5	103	0	.	91
CXCR7	57007	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	237489341	237489341	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CXCR7	NM_020311	exon2	c.A233T	p.D78V	.	.	159	79	171	0	.	1145
CXorf36	79742	bcgsc.ca	37	X	45051113	45051113	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CXorf36	NM_176819	exon2	c.G381A	p.R127R	.	.	183	5	153	0	.	130
CYLD	1540	bcgsc.ca	37	16	50827558	50827558	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	CYLD	NM_015247	exon18	c.2452delA	p.K818fs	.	.	27	3	67	0	.	2444
DCAF12L2	340578	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	X	125299293	125299293	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DCAF12L2	NM_001013628	exon1	c.C615A	p.D205E	.	.	248	44	267	0	.	113
DDX11	1663	ucsc.edu	37	12	31254052	31254052	+	Missense_Mutation	SNP	G	G	C	rs201027785		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DDX11	NM_030653	exon20	c.G2040C	p.E680D	.	.	99	1	119	0	G|0.932;C|0.068	229
DENND2C	163259	bcgsc.ca	37	1	115168554	115168554	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DENND2C	NM_001256404	exon4	c.T52C	p.C18R	.	.	60	4	94	0	.	229
DHX29	54505	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	54563641	54563641	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DHX29	NM_019030	exon22	c.G3304A	p.A1102T	.	.	70	32	66	0	.	229
DICER1	23405	bcgsc.ca	37	14	95590558	95590558	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DICER1	NM_030621	exon9	c.1351delA	p.R451fs	.	.	41	4	79	0	.	961
DMKN	93099	bcgsc.ca	37	19	35996879	35996879	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DMKN	NM_001190348	exon11	c.A1198G	p.T400A	.	.	84	4	68	1	.	155
DNAH14	127602	bcgsc.ca	37	1	225528186	225528186	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DNAH14	NM_001373	exon67	c.C10182A	p.N3394K	.	.	727	18	280	3	.	23
DNAJC5G	285126	ucsc.edu;bcgsc.ca	37	2	27500670	27500670	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DNAJC5G	NM_173650	exon4	c.G162A	p.R54R	.	.	197	87	171	1	.	226
DST	667	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	56497659	56497659	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	DST	NM_001723	exon14	c.A2187G	p.A729A	.	.	128	46	93	0	.	523
EFR3A	23167	bcgsc.ca	37	8	132991670	132991670	+	Splice_Site	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	EFR3A	NM_015137	exon14	c.1575+2T>C	.	.	.	52	4	143	0	.	139
EFTUD2	9343	bcgsc.ca	37	17	42960512	42960512	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	EFTUD2	NM_004247	exon6	c.T441C	p.D147D	.	.	87	4	156	0	.	91
ELAVL2	1993	bcgsc.ca	37	9	23731087	23731087	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ELAVL2	NM_001171195	exon3	c.A266G	p.D89G	.	.	89	4	108	0	.	516
EME1	146956	bcgsc.ca	37	17	48452984	48452984	+	Missense_Mutation	SNP	T	T	C	rs141118056		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	EME1	NM_152463	exon2	c.T415C	p.F139L	.	.	134	8	153	4	T|1.000;C|0.000	227
EML6	400954	bcgsc.ca	37	2	55056512	55056512	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001039753	exon6	c.745delG	p.G249fs	.	.	54	5	92	0	.	.
EML6	400954	bcgsc.ca	37	2	55130534	55130534	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001039753	exon23	c.T3304C	p.S1102P	.	.	74	5	125	0	.	.
EPOR	2057	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	11491862	11491862	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	EPOR	NM_000121	exon5	c.C609A	p.T203T	.	.	25	22	64	0	.	523
ERMP1	79956	hgsc.bcm.edu	37	9	5832863	5832863	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ERMP1	NM_024896	exon1	c.G165A	p.G55G	.	.	5	5	0	0	.	69
ERN1	2081	bcgsc.ca	37	17	62125246	62125246	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ERN1	NM_001433	exon19	c.G2501A	p.S834N	.	.	57	4	81	0	.	784
FAIM	55179	bcgsc.ca	37	3	138338596	138338596	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FAIM	NM_001033031	exon2	c.T28C	p.F10L	.	.	145	5	136	0	.	227
FAM211A	388341	bcgsc.ca	37	17	16347059	16347059	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001113567	exon4	c.878delG	p.G293fs	.	.	44	5	119	0	.	.
FAM228B	375190	bcgsc.ca	37	2	24387078	24387078	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	86	4	78	1	.	.
FARP2	9855	bcgsc.ca	37	2	242375929	242375929	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FARP2	NM_014808	exon12	c.T1134C	p.A378A	.	.	92	4	109	0	.	93
FASN	2194	broad.mit.edu;bcgsc.ca	37	17	80046374	80046374	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FASN	NM_004104	exon16	c.2485delC	p.L829fs	.	.	72	7	73	0	.	90
FAT1	2195	bcgsc.ca	37	4	187538165	187538165	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FAT1	NM_005245	exon11	c.T9069C	p.C3023C	.	.	132	6	190	0	.	34
FAT4	79633	bcgsc.ca	37	4	126240400	126240400	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FAT4	NM_024582	exon1	c.A2834G	p.K945R	.	.	83	5	114	0	.	108
FBLN2	2199	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	3	13612069	13612069	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FBLN2	NM_001998	exon2	c.G214C	p.D72H	.	.	412	255	227	0	.	91
FBN3	84467	bcgsc.ca	37	19	8160964	8160964	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FBN3	NM_032447	exon44	c.A5540G	p.D1847G	.	.	155	5	157	0	.	100
FBXO18	84893	bcgsc.ca	37	10	5963480	5963480	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FBXO18	NM_032807	exon16	c.A2423G	p.E808G	.	.	150	5	184	1	.	228
FBXW4	6468	bcgsc.ca	37	10	103427709	103427709	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FBXW4	NM_022039	exon5	c.G704A	p.G235E	.	.	49	4	98	0	.	226
FOXE1	2304	broad.mit.edu;mdanderson.org	37	9	100616350	100616350	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FOXE1	NM_004473	exon1	c.G154A	p.G52R	.	.	22	7	28	0	.	130
FRMD4B	23150	bcgsc.ca	37	3	69225784	69225784	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	FRMD4B	NM_015123	exon22	c.A2875G	p.N959D	.	.	70	4	80	0	.	72
FTX	100302692	bcgsc.ca	37	X	73327467	73327467	+	RNA	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	167	4	181	1	.	.
GABRA2	2555	bcgsc.ca	37	4	46312234	46312234	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GABRA2	NM_000807	exon6	c.A515G	p.D172G	.	.	109	5	124	0	.	94
GFRA1	2674	bcgsc.ca	37	10	118029096	118029096	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GFRA1	NM_001145453	exon4	c.A337G	p.N113D	.	.	60	5	96	0	.	93
GJB4	127534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	35227120	35227120	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GJB4	NM_153212	exon2	c.C265A	p.L89M	.	.	105	50	123	0	.	92
GLI3	2737	hgsc.bcm.edu	37	7	42005877	42005877	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GLI3	NM_000168	exon15	c.A2794T	p.K932X	.	.	114	9	68	0	.	1149
GMIP	51291	bcgsc.ca	37	19	19751132	19751132	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GMIP	NM_016573	exon6	c.A402G	p.E134E	.	.	47	5	96	0	.	91
GPR107	57720	bcgsc.ca	37	9	132837949	132837949	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GPR107	NM_001136557	exon2	c.T176C	p.F59S	.	.	148	5	164	0	.	91
GPR83	10888	bcgsc.ca	37	11	94113691	94113691	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GPR83	NM_016540	exon4	c.T896C	p.V299A	.	.	123	7	150	0	.	92
GPR84	53831	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	54756956	54756956	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GPR84	NM_020370	exon2	c.T680C	p.V227A	.	.	97	40	95	0	.	523
GRB14	2888	bcgsc.ca	37	2	165350955	165350955	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GRB14	NM_004490	exon13	c.T1462C	p.F488L	.	.	164	7	152	0	.	420
GRIA2	2891	bcgsc.ca	37	4	158254122	158254122	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GRIA2	NM_000826	exon7	c.1034delA	p.E345fs	.	.	48	5	85	0	.	515
GRM8	2918	bcgsc.ca	37	7	126409939	126409939	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GRM8	NM_000845	exon6	c.T1337C	p.I446T	.	.	61	4	128	0	.	581
GSDMC	56169	bcgsc.ca	37	8	130788517	130788517	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	GSDMC	NM_031415	exon3	c.G235A	p.G79R	.	.	79	4	128	0	.	93
GTDC2	84892	bcgsc.ca	37	3	43121560	43121560	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_032806	exon2	c.C1364A	p.P455Q	.	.	159	6	127	1	.	.
GTF2IRD1P1	729156	bcgsc.ca	37	7	66304593	66304593	+	RNA	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	36	5	75	0	.	.
HADH	3033	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	108940796	108940796	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HADH	NM_005327	exon4	c.C520T	p.P174S	.	.	114	55	121	0	.	91
HCRTR2	3062	bcgsc.ca	37	6	55142338	55142338	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HCRTR2	NM_001526	exon5	c.T923G	p.I308S	.	.	178	6	134	1	.	525
HDAC5	10014	bcgsc.ca	37	17	42162409	42162409	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HDAC5	NM_001015053	exon15	c.2168delG	p.G723fs	.	.	30	3	85	0	.	227
HDX	139324	broad.mit.edu;bcgsc.ca	37	X	83724514	83724514	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HDX	NM_144657	exon3	c.A217G	p.T73A	.	.	190	6	195	1	.	132
HERC1	8925	bcgsc.ca	37	15	64017510	64017510	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HERC1	NM_003922	exon18	c.A3549G	p.E1183E	.	.	168	6	119	0	.	666
HERC2P9	440248	ucsc.edu	37	15	28929550	28929550	+	RNA	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	30	2	19	0	.	.
HFM1	164045	bcgsc.ca	37	1	91788716	91788716	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HFM1	NM_001017975	exon22	c.A2468G	p.Q823R	.	.	118	5	107	0	.	112
HNRNPH1	3187	bcgsc.ca	37	5	179041962	179041962	+	Splice_Site	SNP	T	T	C	rs113642265	bycluster	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HNRNPH1	NM_005520	exon15	c.1351-2A>G	.	.	.	120	5	119	0	A|1.000	22
HNRNPH2	3188	bcgsc.ca	37	X	100667256	100667256	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HNRNPH2	NM_001032393	exon2	c.G280C	p.D94H	.	.	275	10	318	1	.	130
HNRNPH3	3189	hgsc.bcm.edu;broad.mit.edu	37	10	70101436	70101436	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HNRNPH3	NM_012207	exon8	c.870delG	p.M290fs	.	.	115	10	133	0	.	70
HNRNPK	3190	hgsc.bcm.edu;broad.mit.edu	37	9	86591918	86591918	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HNRNPK	NM_031262	exon5	c.205delC	p.R69fs	.	.	139	10	102	0	.	227
HR	55806	bcgsc.ca	37	8	21977291	21977291	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HR	NM_018411	exon14	c.2959delC	p.Q987fs	.	.	51	5	85	0	.	154
HRC	3270	bcgsc.ca	37	19	49657916	49657916	+	Silent	SNP	T	T	C	rs7409255		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HRC	NM_002152	exon1	c.A579G	p.E193E	.	.	139	24	163	19	.	91
HSFY1P1	27437	bcgsc.ca	37	22	17309880	17309880	+	RNA	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	33	3	71	0	.	.
HSPG2	3339	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	22183660	22183660	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HSPG2	NM_005529	exon44	c.G5423A	p.R1808H	.	.	202	88	235	0	.	141
HTRA2	27429	bcgsc.ca	37	2	74757428	74757428	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HTRA2	NM_013247	exon1	c.295delT	p.S99fs	.	.	37	4	73	0	.	91
HTRA2	27429	broad.mit.edu;mdanderson.org	37	2	74757144	74757144	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HTRA2	NM_013247	exon1	c.C11T	p.P4L	.	.	17	5	25	0	.	91
HYDIN	54768	bcgsc.ca	37	16	70902659	70902659	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	HYDIN	NM_001270974	exon66	c.11124delC	p.D3708fs	.	.	57	4	88	0	.	92
IDE	3416	bcgsc.ca	37	10	94269834	94269834	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	IDE	NM_004969	exon6	c.870delA	p.E290fs	.	.	32	4	74	0	.	92
IRAK2	3656	bcgsc.ca	37	3	10251316	10251316	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	IRAK2	NM_001570	exon4	c.T468C	p.P156P	.	.	87	6	85	0	.	574
ITGA4	3676	bcgsc.ca	37	2	182386952	182386952	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ITGA4	NM_000885	exon18	c.A1957G	p.S653G	.	.	82	4	72	0	.	230
ITGA7	3679	bcgsc.ca	37	12	56089358	56089358	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ITGA7	NM_001144996	exon14	c.C1963A	p.R655S	.	.	255	9	255	2	.	229
ITIH5	80760	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	7608182	7608182	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ITIH5	NM_030569	exon13	c.G2338T	p.V780L	.	.	158	64	198	0	.	92
IZUMO2	126123	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	50666320	50666320	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	IZUMO2	NM_152358	exon1	c.C132T	p.F44F	.	.	182	76	197	0	.	90
JUND	3727	bcgsc.ca	37	19	18391967	18391967	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	JUND	NM_005354	exon1	c.328delT	p.S110fs	.	.	15	3	50	0	.	846
KANK4	163782	bcgsc.ca	37	1	62740066	62740066	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KANK4	NM_181712	exon3	c.G710C	p.G237A	.	.	303	7	327	2	.	74
KANSL1	284058	bcgsc.ca	37	17	44117166	44117166	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001193466	exon8	c.2105delA	p.K702fs	.	.	79	8	172	1	.	.
KCNQ3	3786	bcgsc.ca	37	8	133198356	133198356	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KCNQ3	NM_004519	exon2	c.A459G	p.G153G	.	.	69	5	157	0	.	138
KDM3A	55818	bcgsc.ca	37	2	86693761	86693761	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KDM3A	NM_001146688	exon10	c.A1274G	p.K425R	.	.	146	6	139	0	.	291
KDM6B	23135	broad.mit.edu;bcgsc.ca	37	17	7753448	7753448	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KDM6B	NM_001080424	exon13	c.G3626A	p.R1209Q	.	.	81	5	163	0	.	205
KIAA0196	9897	bcgsc.ca	37	8	126061309	126061309	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIAA0196	NM_014846	exon19	c.A2318G	p.E773G	.	.	89	4	145	1	.	92
KIAA1109	84162	bcgsc.ca	37	4	123283371	123283371	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIAA1109	NM_015312	exon84	c.14987delA	p.E4996fs	.	.	41	4	69	0	.	80
KIAA1432	57589	ucsc.edu;bcgsc.ca;mdanderson.org	37	9	5742878	5742878	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIAA1432	NM_001206557	exon9	c.A911G	p.N304S	.	.	145	73	156	2	.	90
KIAA1551	55196	hgsc.bcm.edu;broad.mit.edu	37	12	32138119	32138119	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_018169	exon4	c.4230delT	p.S1410fs	.	.	163	10	156	0	.	.
KIAA1841	84542	bcgsc.ca	37	2	61349264	61349264	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIAA1841	NM_001129993	exon22	c.T2124C	p.S708S	.	.	50	4	86	0	.	90
KIF13A	63971	bcgsc.ca	37	6	17794508	17794508	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIF13A	NM_001105567	exon25	c.A3194G	p.K1065R	.	.	190	6	112	0	.	137
KIF22	3835	bcgsc.ca	37	16	29810070	29810070	+	Splice_Site	SNP	T	T	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KIF22	NM_007317	exon4	c.549+2T>G	.	.	.	84	5	109	0	.	68
KLHL22	84861	bcgsc.ca	37	22	20825741	20825741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KLHL22	NM_032775	exon3	c.T289C	p.S97P	.	.	130	5	164	0	.	278
KRBA1	84626	bcgsc.ca	37	7	149418039	149418039	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KRBA1	.	.	.	.	.	.	56	4	97	2	.	91
KRT84	3890	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	12	52771877	52771877	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	KRT84	NM_033045	exon9	c.G1744T	p.G582C	.	.	163	72	210	0	.	91
LDHC	3948	bcgsc.ca	37	11	18467858	18467858	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LDHC	NM_002301	exon7	c.A812G	p.H271R	.	.	110	5	84	0	.	226
LEPROTL1	23484	bcgsc.ca	37	8	29959445	29959445	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LEPROTL1	NM_001128208	exon2	c.C48T	p.I16I	.	.	35	4	91	0	.	90
LPHN3	23284	bcgsc.ca	37	4	62598760	62598760	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LPHN3	NM_015236	exon5	c.T683C	p.I228T	.	.	74	5	98	0	.	508
LRRC8E	80131	bcgsc.ca	37	19	7964734	7964734	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LRRC8E	NM_001268284	exon4	c.A1327G	p.R443G	.	.	51	4	60	1	.	92
LRRN3	54674	bcgsc.ca	37	7	110764137	110764137	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LRRN3	NM_018334	exon2	c.1309delG	p.G437fs	.	.	27	4	74	0	.	154
LTF	4057	bcgsc.ca	37	3	46486894	46486894	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LTF	NM_002343	exon12	c.A1391G	p.D464G	.	.	71	3	101	1	.	703
LUZP2	338645	bcgsc.ca	37	11	25071662	25071662	+	Missense_Mutation	SNP	T	T	C	rs199960455		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	LUZP2	NM_001009909	exon10	c.T844C	p.C282R	.	.	72	4	74	0	T|0.999;C|0.000	92
MAN2A1	4124	ucsc.edu;bcgsc.ca	37	5	109091087	109091087	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MAN2A1	NM_002372	exon5	c.A765G	p.E255E	.	.	143	68	150	2	.	92
MAN2C1	4123	bcgsc.ca	37	15	75648518	75648518	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MAN2C1	NM_001256494	exon25	c.T2980C	p.Y994H	.	.	146	5	120	0	.	90
MAN2C1	4123	bcgsc.ca	37	15	75653703	75653703	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MAN2C1	NM_001256494	exon11	c.A1238G	p.E413G	.	.	72	5	90	0	.	90
MAP1B	4131	hgsc.bcm.edu;broad.mit.edu	37	5	71493243	71493243	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MAP1B	NM_005909	exon5	c.4061delA	p.E1354fs	.	.	142	10	135	0	.	155
MAPK9	5601	bcgsc.ca	37	5	179666939	179666939	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MAPK9	NM_002752	exon10	c.A1045G	p.I349V	.	.	168	5	174	0	.	1402
MC5R	4161	bcgsc.ca	37	18	13825784	13825784	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MC5R	NM_005913	exon1	c.T20C	p.L7P	.	.	160	5	134	1	.	526
MCPH1	79648	bcgsc.ca	37	8	6293638	6293638	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MCPH1	NM_001172575	exon5	c.391delT	p.F131fs	.	.	59	6	101	0	.	229
MED13	9969	bcgsc.ca	37	17	60088139	60088139	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MED13	NM_005121	exon9	c.A1739G	p.D580G	.	.	247	6	245	0	.	136
MED25	81857	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	50333046	50333046	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MED25	NM_030973	exon6	c.G529A	p.G177R	.	.	167	83	147	0	.	91
MFSD4	148808	bcgsc.ca	37	1	205561373	205561373	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MFSD4	NM_181644	exon7	c.C1255T	p.P419S	.	.	416	9	228	2	.	92
MFSD5	84975	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	53646714	53646714	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MFSD5	NM_001170790	exon2	c.C416T	p.A139V	.	.	174	82	149	0	.	93
MIR133B	442890	bcgsc.ca	37	6	52013751	52013751	+	RNA	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	67	4	81	0	.	.
MORC1	27136	bcgsc.ca	37	3	108705728	108705728	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MORC1	NM_014429	exon22	c.A2256G	p.Q752Q	.	.	79	6	69	0	.	98
MSX1	4487	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	4	4864457	4864457	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MSX1	NM_002448	exon2	c.C499T	p.R167C	.	.	91	37	83	0	.	90
MTF2	22823	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	93545089	93545089	+	Splice_Site	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MTF2	NM_001164392	exon1	c.5+1G>T	.	.	.	104	53	127	0	.	92
MTPN	136319	bcgsc.ca	37	7	135614722	135614722	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MTPN	NM_145808	exon4	c.309delC	p.T103fs	.	.	32	4	73	0	.	90
MTTP	4547	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	100532580	100532580	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MTTP	NM_000253	exon15	c.C1959T	p.Y653Y	.	.	142	68	144	0	.	93
MUC16	94025	bcgsc.ca	37	19	9056872	9056872	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MUC16	NM_024690	exon3	c.T30574C	p.S10192P	.	.	160	6	181	0	.	566
MYH4	4622	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	10354170	10354170	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MYH4	NM_017533	exon29	c.C3908A	p.S1303Y	.	.	145	122	250	0	.	102
MYO5B	4645	bcgsc.ca	37	18	47455924	47455924	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	MYO5B	NM_001080467	exon17	c.T2048A	p.V683E	.	.	63	4	62	0	.	72
NBEA	26960	bcgsc.ca	37	13	35756614	35756614	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NBEA	NM_015678	exon29	c.A4780G	p.S1594G	.	.	87	4	127	0	.	144
NCF2	4688	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	183532683	183532683	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NCF2	NM_001127651	exon13	c.A1064C	p.K355T	.	.	301	57	135	0	.	93
NCOA6	23054	bcgsc.ca	37	20	33345744	33345744	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NCOA6	NM_014071	exon7	c.G807A	p.Q269Q	.	.	149	6	140	2	.	292
NDRG4	65009	bcgsc.ca	37	16	58540480	58540480	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NDRG4	NM_001130487	exon9	c.634delA	p.T212fs	.	.	40	4	99	0	.	91
NDST2	8509	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	75566200	75566200	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NDST2	NM_003635	exon6	c.T1281C	p.A427A	.	.	60	28	95	0	.	91
NEK6	10783	hgsc.bcm.edu;bcgsc.ca	37	9	127101926	127101926	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NEK6	NM_001166171	exon9	c.G801T	p.L267L	.	.	238	10	257	0	.	334
NEK9	91754	bcgsc.ca	37	14	75563856	75563856	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NEK9	NM_033116	exon17	c.T2120C	p.L707P	.	.	70	4	90	0	.	359
NELFA	7469	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	1993397	1993397	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_005663	exon2	c.T289G	p.S97A	.	.	133	44	121	0	.	.
NFASC	23114	hgsc.bcm.edu;broad.mit.edu	37	1	204971735	204971735	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NFASC	NM_001005388	exon27	c.3148delA	p.K1050fs	.	.	213	16	112	0	.	139
NLGN4X	57502	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	X	6069292	6069292	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NLGN4X	NM_181332	exon2	c.G216T	p.Q72H	.	.	305	138	382	0	.	195
NMBR	4829	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	6	142400004	142400004	+	Silent	SNP	C	C	T	rs149123905		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NMBR	NM_002511	exon2	c.G459A	p.T153T	.	.	162	20	134	0	C|1.000;T|0.000	946
NOL10	79954	hgsc.bcm.edu;broad.mit.edu	37	2	10729763	10729763	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_024894	exon18	c.1537delA	p.I513fs	.	.	142	10	122	0	.	.
NPR2	4882	bcgsc.ca	37	9	35793940	35793940	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NPR2	NM_003995	exon2	c.T713C	p.L238P	.	.	255	7	257	0	.	335
NR3C2	4306	bcgsc.ca	37	4	149356663	149356663	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NR3C2	NM_001166104	exon2	c.1350delT	p.F450fs	.	.	59	6	74	0	.	154
NSMAF	8439	bcgsc.ca	37	8	59514660	59514660	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NSMAF	NM_001144772	exon14	c.A1175G	p.K392R	.	.	88	4	131	0	.	91
NUDCD1	84955	bcgsc.ca	37	8	110283286	110283286	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	NUDCD1	NM_032869	exon8	c.A1247G	p.E416G	.	.	56	4	131	0	.	227
NXPE1	120400	bcgsc.ca	37	11	114393611	114393611	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_152315	exon5	c.A672G	p.K224K	.	.	97	4	118	0	.	.
OGFOD3	79701	bcgsc.ca	37	17	80373502	80373502	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_175902	exon2	c.A76G	p.T26A	.	.	39	4	40	0	.	.
OR11G2	390439	ucsc.edu;bcgsc.ca	37	14	20666407	20666407	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR11G2	NM_001005503	exon1	c.G913C	p.E305Q	.	.	217	115	240	2	.	70
OR14A16	284532	hgsc.bcm.edu	37	1	247978543	247978543	+	Silent	SNP	G	G	T	rs200138400		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR14A16	NM_001001966	exon1	c.C489A	p.S163S	.	.	212	16	74	0	.	46
OR2W1	26692	hgsc.bcm.edu	37	6	29012812	29012812	+	Silent	SNP	A	A	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR2W1	NM_030903	exon1	c.T141G	p.L47L	.	.	408	37	246	0	.	93
OR4C12	283093	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	50003747	50003747	+	Silent	SNP	A	A	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR4C12	NM_001005270	exon1	c.T291A	p.A97A	.	.	210	99	226	0	.	93
OR5V1	81696	ucsc.edu;bcgsc.ca;mdanderson.org	37	6	29323162	29323162	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR5V1	NM_030876	exon1	c.G811T	p.D271Y	.	.	132	67	93	1	.	72
OR5W2	390148	bcgsc.ca	37	11	55681169	55681169	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	OR5W2	NM_001001960	exon1	c.T890C	p.V297A	.	.	129	5	116	0	.	70
OTOGL	283310	bcgsc.ca	37	12	80722448	80722448	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_173591	exon35	c.T4176C	p.V1392V	.	.	124	6	149	0	.	.
PACS2	23241	bcgsc.ca	37	14	105858978	105858978	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PACS2	NM_001100913	exon23	c.2278delA	p.M760fs	.	.	41	4	93	0	.	69
PARP14	54625	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	122418450	122418450	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PARP14	NM_017554	exon6	c.G1049A	p.R350H	.	.	141	59	140	0	.	525
PER2	8864	bcgsc.ca	37	2	239171593	239171593	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PER2	NM_022817	exon10	c.A1153G	p.I385V	.	.	69	4	82	0	.	154
PGM5P2	595135	broad.mit.edu	37	9	69084916	69084916	+	RNA	SNP	A	A	T	rs79926676		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	80	5	99	1	A|0.500;T|0.500	.
PI4KAP2	375133	broad.mit.edu	37	22	21830312	21830312	+	RNA	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PI4KAP2	.	.	.	.	.	.	85	6	103	1	.	68
PITRM1	10531	bcgsc.ca	37	10	3202465	3202465	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PITRM1	NM_001242307	exon8	c.A849G	p.E283E	.	.	135	5	127	0	.	91
PIWIL2	55124	bcgsc.ca	37	8	22173796	22173796	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PIWIL2	NM_001135721	exon19	c.2247delC	p.D749fs	.	.	36	4	85	0	.	91
PLEKHA1	59338	bcgsc.ca	37	10	124172507	124172507	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PLEKHA1	NM_001195608	exon7	c.A414G	p.Q138Q	.	.	80	4	179	0	.	226
PLEKHA5	54477	bcgsc.ca	37	12	19518932	19518932	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PLEKHA5	NM_001256470	exon30	c.C3643T	p.P1215S	.	.	48	4	34	0	.	227
PLEKHG1	57480	bcgsc.ca	37	6	151121887	151121887	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PLEKHG1	NM_001029884	exon7	c.A662G	p.N221S	.	.	168	7	149	1	.	92
PLEKHS1	79949	bcgsc.ca	37	10	115526208	115526208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_024889	exon3	c.A67G	p.K23E	.	.	79	4	178	0	.	.
PNMA2	10687	bcgsc.ca	37	8	26365734	26365734	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PNMA2	NM_007257	exon3	c.T538C	p.S180P	.	.	69	4	119	1	.	90
POM121C	100101267	bcgsc.ca	37	7	75053478	75053478	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001099415	exon12	c.C902A	p.P301Q	.	.	377	13	681	5	.	.
POMGNT1	55624	bcgsc.ca	37	1	46658210	46658210	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	POMGNT1	NM_017739	exon15	c.A1264G	p.I422V	.	.	203	6	132	0	.	91
PPFIA3	8541	bcgsc.ca	37	19	49633308	49633308	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PPFIA3	NM_003660	exon6	c.A641G	p.K214R	.	.	74	4	91	0	.	226
PPP1R16B	26051	bcgsc.ca	37	20	37518290	37518290	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PPP1R16B	NM_001172735	exon3	c.A303G	p.G101G	.	.	102	6	134	1	.	228
PPP2R5C	5527	bcgsc.ca	37	14	102252487	102252487	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PPP2R5C	NM_001161726	exon3	c.A226G	p.N76D	.	.	100	4	178	0	.	659
PPP3CB	5532	bcgsc.ca	37	10	75206313	75206313	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PPP3CB	NM_001142354	exon11	c.A1208G	p.K403R	.	.	99	4	79	0	.	226
PRDM1	639	hgsc.bcm.edu;broad.mit.edu	37	6	106553568	106553568	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PRDM1	NM_001198	exon5	c.1533delC	p.S511fs	.	.	147	10	119	0	.	862
PRKAG2	51422	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	151372542	151372542	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PRKAG2	NM_016203	exon4	c.A648G	p.P216P	.	.	71	59	163	0	.	658
PTGIS	5740	broad.mit.edu;bcgsc.ca	37	20	48166687	48166687	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PTGIS	NM_000961	exon2	c.114delC	p.P38fs	.	.	83	8	90	0	.	93
PTK2B	2185	bcgsc.ca	37	8	27292036	27292036	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PTK2B	NM_173174	exon18	c.1152delG	p.L384fs	.	.	42	4	94	0	.	1378
PTPRK	5796	bcgsc.ca	37	6	128563680	128563680	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PTPRK	NM_001135648	exon4	c.T563C	p.L188P	.	.	159	6	103	0	.	231
PTPRN2	5799	bcgsc.ca	37	7	158109614	158109614	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PTPRN2	NM_130843	exon3	c.174delT	p.F58fs	.	.	24	5	46	0	.	295
PXDNL	137902	bcgsc.ca	37	8	52567308	52567308	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	PXDNL	NM_144651	exon2	c.177delT	p.F59fs	.	.	44	4	72	0	.	70
QARS	5859	hgsc.bcm.edu;broad.mit.edu	37	3	49140816	49140816	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	QARS	NM_005051	exon5	c.478delG	p.A160fs	.	.	143	12	122	0	.	91
RABGGTB	5876	bcgsc.ca	37	1	76257894	76257894	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RABGGTB	NM_004582	exon7	c.T608C	p.I203T	.	.	106	4	79	0	.	227
RAPGEF5	9771	bcgsc.ca	37	7	22165263	22165263	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RAPGEF5	NM_012294	exon25	c.A2036G	p.D679G	.	.	135	6	160	1	.	206
RASSF10	644943	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	13031942	13031942	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001080521	exon1	c.G819T	p.V273V	.	.	364	169	454	0	.	.
RAVER2	55225	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	65243382	65243382	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RAVER2	NM_018211	exon3	c.A393C	p.K131N	.	.	163	79	170	0	.	135
RB1	5925	bcgsc.ca	37	13	49050911	49050911	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RB1	NM_000321	exon25	c.2595delA	p.G865fs	.	.	32	4	89	0	.	3784
RBM48	84060	bcgsc.ca	37	7	92163807	92163807	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_032120	exon4	c.T540C	p.C180C	.	.	65	4	115	0	.	.
RCN2	5955	bcgsc.ca	37	15	77241459	77241459	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RCN2	NM_001271837	exon8	c.T904C	p.S302P	.	.	86	4	59	0	.	90
REG1P	5969	bcgsc.ca	37	2	79362864	79362864	+	RNA	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	9	3	35	0	.	.
REXO4	57109	bcgsc.ca	37	9	136277482	136277482	+	Missense_Mutation	SNP	T	T	G	rs2285487	byfrequency;alternate_allele	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	REXO4	NM_020385	exon4	c.A847C	p.T283P	.	.	147	5	159	3	T|0.944;C|0.056	90
RFX5	5993	hgsc.bcm.edu;broad.mit.edu	37	1	151318753	151318753	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RFX5	NM_000449	exon3	c.44delG	p.G15fs	.	.	249	16	119	0	.	91
RHBDF2	79651	hgsc.bcm.edu;bcgsc.ca	37	17	74473785	74473787	+	In_Frame_Del	DEL	TCC	TCC	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RHBDF2	NM_024599	exon7	c.840_842del	p.280_281del	.	.	40	28	88	0	.	90
RNR2	6053	broad.mit.edu	37	MT	2098	2098	+	RNA	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	4	2	15	0	.	.
RP1L1	94137	bcgsc.ca	37	8	10480616	10480616	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RP1L1	NM_178857	exon2	c.A96G	p.P32P	.	.	71	4	135	0	.	139
RP1L1	94137	broad.mit.edu;bcgsc.ca;mdanderson.org	37	8	10480350	10480350	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RP1L1	NM_178857	exon2	c.A362G	p.E121G	.	.	26	4	63	1	.	139
RPS6KA3	6197	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	X	20194413	20194413	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RPS6KA3	NM_004586	exon13	c.G1057T	p.D353Y	.	.	356	146	317	0	.	1504
RRBP1	6238	bcgsc.ca	37	20	17640671	17640671	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	RRBP1	NM_004587	exon2	c.A482G	p.Q161R	.	.	77	5	91	0	.	92
SCAMP5	192683	hgsc.bcm.edu;broad.mit.edu	37	15	75308993	75308993	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SCAMP5	NM_001178111	exon5	c.196delG	p.G66fs	.	.	156	10	125	0	.	23
SCARA5	286133	bcgsc.ca	37	8	27823939	27823939	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SCARA5	NM_173833	exon3	c.T233C	p.I78T	.	.	113	5	174	0	.	91
SCN1A	6323	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	166854614	166854614	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SCN1A	NM_001165963	exon23	c.G4410A	p.G1470G	.	.	230	102	254	0	.	147
SCN3A	6328	bcgsc.ca	37	2	165984172	165984172	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SCN3A	NM_006922	exon18	c.G3362A	p.S1121N	.	.	78	4	80	0	.	141
SEMA3E	9723	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	83029465	83029465	+	Silent	SNP	T	T	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SEMA3E	NM_012431	exon11	c.A1245C	p.I415I	.	.	178	157	403	0	.	93
SERPINA12	145264	bcgsc.ca	37	14	94964705	94964705	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SERPINA12	NM_173850	exon3	c.30delT	p.F10fs	.	.	55	6	87	0	.	310
SERPINA4	5267	bcgsc.ca	37	14	95030110	95030110	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SERPINA4	NM_006215	exon2	c.291delC	p.S97fs	.	.	38	4	61	0	.	230
SERPINA6	866	bcgsc.ca	37	14	94776279	94776279	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SERPINA6	NM_001756	exon3	c.A678G	p.T226T	.	.	78	4	127	0	.	653
SETDB2	83852	bcgsc.ca	37	13	50034326	50034326	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SETDB2	NM_001160308	exon2	c.T100C	p.S34P	.	.	50	4	80	0	.	91
SETX	23064	bcgsc.ca	37	9	135218139	135218139	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SETX	NM_015046	exon5	c.T436C	p.S146P	.	.	41	4	54	0	.	93
SGOL2	151246	bcgsc.ca	37	2	201400866	201400866	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SGOL2	NM_001160033	exon4	c.387+1G>A	.	.	.	85	4	87	0	.	94
SIGLEC1	6614	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	20	3672111	3672111	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SIGLEC1	NM_023068	exon17	c.C4467T	p.H1489H	.	.	359	172	364	0	.	167
SIRPD	128646	bcgsc.ca	37	20	1532596	1532596	+	Silent	SNP	G	G	C	rs144302855	alternate_allele	TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SIRPD	NM_178460	exon2	c.C162G	p.P54P	.	.	165	7	164	0	G|1.000;A|0.000	227
SLC18A1	6570	bcgsc.ca	37	8	20007210	20007210	+	Nonsense_Mutation	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC18A1	NM_003053	exon12	c.1123delG	p.V375X	.	.	48	5	91	0	.	92
SLC18A2	6571	bcgsc.ca	37	10	119015120	119015120	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC18A2	NM_003054	exon9	c.A847G	p.T283A	.	.	33	4	48	0	.	90
SLC25A30	253512	bcgsc.ca	37	13	45973083	45973083	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC25A30	NM_001010875	exon8	c.T745C	p.L249L	.	.	62	4	116	0	.	135
SLC38A8	146167	bcgsc.ca	37	16	84075659	84075659	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC38A8	NM_001080442	exon1	c.104delA	p.K35fs	.	.	32	4	70	0	.	68
SLC45A4	57210	bcgsc.ca	37	8	142227227	142227227	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC45A4	NM_001080431	exon5	c.1538delG	p.G513fs	.	.	26	6	59	0	.	70
SLC45A4	57210	bcgsc.ca	37	8	142228138	142228138	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLC45A4	NM_001080431	exon4	c.1448delG	p.G483fs	.	.	29	4	63	0	.	70
SLITRK4	139065	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	142717432	142717432	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SLITRK4	NM_001184750	exon2	c.T1493C	p.L498S	.	.	245	114	274	0	.	193
SMARCA2	6595	bcgsc.ca	37	9	2182178	2182178	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SMARCA2	NM_003070	exon31	c.A4397G	p.D1466G	.	.	78	5	83	1	.	653
SMIM15	643155	bcgsc.ca	37	5	60455998	60455998	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001048249	exon3	c.A1G	p.M1V	.	.	134	6	178	1	.	.
SOGA1	140710	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	35437068	35437068	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_080627	exon8	c.C2662A	p.Q888K	.	.	61	25	88	0	.	.
SORBS2	8470	bcgsc.ca	37	4	186567931	186567931	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SORBS2	NM_001145673	exon11	c.A1112G	p.D371G	.	.	69	4	75	0	.	91
SORCS1	114815	bcgsc.ca	37	10	108380292	108380292	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SORCS1	NM_001206572	exon20	c.T2690C	p.L897P	.	.	164	6	164	0	.	153
SPEN	23013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	16255127	16255127	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SPEN	NM_015001	exon11	c.G2392C	p.D798H	.	.	43	16	45	0	.	298
SPOCD1	90853	bcgsc.ca	37	1	32279602	32279602	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SPOCD1	NM_144569	exon2	c.T1333C	p.S445P	.	.	195	6	214	2	.	158
SRGAP2D	100996712	bcgsc.ca	37	1	121116689	121116689	+	Silent	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001271887	exon3	c.C246T	p.H82H	.	.	213	13	211	2	.	.
SRRM2	23524	bcgsc.ca	37	16	2814503	2814503	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SRRM2	NM_016333	exon11	c.A3974G	p.N1325S	.	.	75	4	73	0	.	93
SRRT	51593	bcgsc.ca	37	7	100482657	100482657	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SRRT	NM_001128853	exon9	c.1155delG	p.E385fs	.	.	33	3	78	0	.	92
ST7L	54879	bcgsc.ca	37	1	113125058	113125058	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ST7L	NM_138729	exon8	c.893delG	p.R298fs	.	.	28	3	67	0	.	90
STOML3	161003	bcgsc.ca	37	13	39542653	39542653	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	STOML3	NM_145286	exon6	c.A535G	p.T179A	.	.	50	4	96	0	.	91
STXBP3	6814	bcgsc.ca	37	1	109342913	109342913	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	STXBP3	NM_007269	exon17	c.T1521C	p.G507G	.	.	84	4	60	0	.	93
SULT6B1	391365	bcgsc.ca	37	2	37402285	37402285	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SULT6B1	NM_001032377	exon5	c.A500G	p.D167G	.	.	293	8	263	0	.	91
SVEP1	79987	bcgsc.ca	37	9	113171160	113171160	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SVEP1	NM_153366	exon38	c.T6720C	p.S2240S	.	.	74	4	42	0	.	75
SYCE1L	100130958	bcgsc.ca	37	16	77243338	77243338	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_001129979	exon6	c.A329G	p.H110R	.	.	44	4	93	1	.	.
SYCP2	10388	bcgsc.ca	37	20	58487429	58487429	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SYCP2	NM_014258	exon12	c.A875G	p.E292G	.	.	85	4	77	0	.	525
SYNE1	23345	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	152740820	152740820	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	SYNE1	NM_033071	exon40	c.C5326A	p.Q1776K	.	.	247	79	189	0	.	607
TAF1B	9014	bcgsc.ca	37	2	10059168	10059168	+	Splice_Site	SNP	A	A	G	rs113138392		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TAF1B	NM_005680	exon13	c.1272-2A>G	.	.	.	93	5	101	0	A|0.500;G|0.500	92
TAF6	6878	bcgsc.ca	37	7	99707891	99707891	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TAF6	NM_001190415	exon11	c.G1201A	p.V401M	.	.	51	4	119	0	.	91
TCEANC	170082	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	X	13681572	13681572	+	Silent	SNP	T	T	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TCEANC	NM_152634	exon4	c.T1035A	p.L345L	.	.	150	72	158	0	.	41
TECPR2	9895	bcgsc.ca	37	14	102904465	102904465	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TECPR2	NM_001172631	exon10	c.2501delG	p.C834fs	.	.	49	5	82	0	.	92
THSD7A	221981	bcgsc.ca	37	7	11633083	11633083	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	THSD7A	NM_015204	exon3	c.A1069G	p.I357V	.	.	111	5	143	0	.	71
TMEM131	23505	bcgsc.ca	37	2	98409883	98409883	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TMEM131	NM_015348	exon30	c.A3520G	p.I1174V	.	.	129	5	107	0	.	74
TMEM215	401498	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	32784212	32784212	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TMEM215	NM_212558	exon2	c.G31T	p.G11W	.	.	432	175	390	1	.	90
TNFRSF10A	8797	bcgsc.ca	37	8	23082543	23082543	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TNFRSF10A	NM_003844	exon1	c.32delG	p.G11fs	.	.	23	3	68	0	.	1086
TNR	7143	ucsc.edu;bcgsc.ca;mdanderson.org	37	1	175360557	175360557	+	Silent	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TNR	NM_003285	exon7	c.G1374T	p.V458V	.	.	184	135	92	1	.	324
TNRC18	84629	hgsc.bcm.edu;broad.mit.edu	37	7	5410486	5410486	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TNRC18	NM_001080495	exon11	c.3739delG	p.V1247fs	.	.	146	10	169	0	.	46
TP53	7157	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	7577565	7577565	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	TP53,NS,carcinoma,-1	TP53	NM_000546	exon7	c.A716G	p.N239S	.	.	111	96	266	0	.	70225
TP53BP1	7158	broad.mit.edu	37	15	43700139	43700139	+	Splice_Site	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TP53BP1	NM_005657	exon28	c.5731+2T>C	.	.	.	29	3	22	0	.	294
TPM4	7171	bcgsc.ca	37	19	16192755	16192755	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TPM4	NM_001145160	exon3	c.273delC	p.R91fs	.	.	40	4	76	0	.	316
TREH	11181	bcgsc.ca	37	11	118529045	118529045	+	Splice_Site	SNP	C	C	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TREH	.	.	.	.	.	.	281	22	310	13	.	46
TROAP	10024	ucsc.edu;bcgsc.ca;mdanderson.org	37	12	49723711	49723711	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TROAP	NM_005480	exon12	c.G1236A	p.P412P	.	.	159	75	143	2	.	91
TSHZ3	57616	bcgsc.ca	37	19	31767812	31767812	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TSHZ3	NM_020856	exon2	c.A2887G	p.T963A	.	.	149	5	161	0	.	232
TTC22	55001	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	55248004	55248004	+	Silent	SNP	G	G	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TTC22	NM_001114108	exon6	c.C1167T	p.I389I	.	.	68	24	42	0	.	90
TTN	7273	bcgsc.ca	37	2	179431270	179431270	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TTN	NM_001267550	exon326	c.A79589G	p.D26530G	.	.	105	6	96	0	.	636
TTN	7273	bcgsc.ca	37	2	179589134	179589134	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TTN	NM_001267550	exon72	c.A20968G	p.S6990G	.	.	171	6	186	1	.	636
TTN	7273	bcgsc.ca	37	2	179596303	179596303	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TTN	NM_001267550	exon59	c.A17190G	p.P5730P	.	.	63	4	66	0	.	636
TTR	7276	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	29172906	29172906	+	Silent	SNP	T	T	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TTR	NM_000371	exon2	c.T117A	p.A39A	.	.	144	63	145	0	.	91
TUBGCP6	85378	bcgsc.ca	37	22	50664261	50664261	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	TUBGCP6	NM_020461	exon10	c.A1945G	p.R649G	.	.	69	5	119	5	.	93
UBR1	197131	hgsc.bcm.edu;broad.mit.edu	37	15	43363075	43363075	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	UBR1	NM_174916	exon5	c.577delA	p.I193fs	.	.	134	12	76	0	.	91
UBR3	130507	bcgsc.ca	37	2	170734035	170734035	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	UBR3	NM_172070	exon4	c.T876C	p.S292S	.	.	74	4	72	0	.	68
ULK4	54986	bcgsc.ca	37	3	41996212	41996212	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ULK4	NM_017886	exon2	c.A40G	p.S14G	.	.	233	7	228	0	.	297
UNC79	57578	bcgsc.ca	37	14	94158267	94158267	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_020818	exon47	c.T7031C	p.L2344P	.	.	72	4	159	0	.	.
USP15	9958	bcgsc.ca	37	12	62696641	62696641	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	USP15	NM_001252078	exon3	c.T288C	p.G96G	.	.	112	5	96	0	.	1084
USP33	23032	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	78183652	78183652	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	USP33	NM_015017	exon18	c.A1911G	p.L637L	.	.	175	84	196	0	.	659
USP50	373509	bcgsc.ca	37	15	50833395	50833395	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	USP50	NM_203494	exon4	c.A511G	p.T171A	.	.	150	5	121	0	.	658
UTP18	51096	bcgsc.ca	37	17	49365429	49365429	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	UTP18	NM_016001	exon11	c.T1368C	p.S456S	.	.	180	6	164	0	.	90
VIPR2	7434	bcgsc.ca	37	7	158851181	158851181	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VIPR2	NM_003382	exon5	c.446delG	p.C149fs	.	.	35	3	76	0	.	91
VPS13B	157680	bcgsc.ca	37	8	100791078	100791078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VPS13B	NM_017890	exon42	c.A7673G	p.E2558G	.	.	98	4	195	0	.	301
VPS8	23355	broad.mit.edu;bcgsc.ca	37	3	184654112	184654112	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VPS8	NM_001009921	exon34	c.2977delA	p.K993fs	.	.	72	7	72	0	.	91
VSIG1	340547	bcgsc.ca	37	X	107288380	107288380	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VSIG1	NM_001170553	exon1	c.A20G	p.K7R	.	.	52	4	64	0	.	132
VSX1	30813	hgsc.bcm.edu;broad.mit.edu	37	20	25057157	25057157	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VSX1	NM_014588	exon5	c.A838G	p.R280G	.	.	97	4	88	0	.	90
VWA5A	4013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	124013240	124013240	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	VWA5A	NM_014622	exon16	c.T2115C	p.G705G	.	.	90	40	103	0	.	92
WAS	7454	bcgsc.ca	37	X	48544002	48544002	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WAS	NM_000377	exon3	c.T340C	p.F114L	.	.	186	7	251	2	.	563
WDR44	54521	bcgsc.ca;mdanderson.org	37	X	117566745	117566745	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WDR44	NM_001184965	exon13	c.T1739A	p.V580E	.	.	305	18	295	0	.	133
WDR62	284403	bcgsc.ca	37	19	36558212	36558212	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WDR62	NM_173636	exon6	c.A566G	p.D189G	.	.	162	5	165	0	.	90
WDR70	55100	hgsc.bcm.edu;broad.mit.edu	37	5	37752658	37752658	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WDR70	NM_018034	exon18	c.1948delA	p.K650fs	.	.	185	11	83	0	.	187
WDR72	256764	bcgsc.ca	37	15	54003562	54003562	+	Silent	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WDR72	NM_182758	exon8	c.T828C	p.G276G	.	.	206	8	178	0	.	92
WEE2	494551	bcgsc.ca	37	7	141408580	141408580	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WEE2	NM_001105558	exon1	c.22delA	p.K8fs	.	.	40	4	79	0	.	305
WIF1	11197	hgsc.bcm.edu;broad.mit.edu	37	12	65514293	65514293	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WIF1	NM_007191	exon2	c.192delA	p.A64fs	.	.	164	10	142	0	.	1110
WNK3	65267	bcgsc.ca	37	X	54265313	54265313	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	WNK3	NM_020922	exon18	c.A3871G	p.K1291E	.	.	95	4	84	0	.	441
XAF1	54739	bcgsc.ca	37	17	6663029	6663029	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	XAF1	NM_017523	exon3	c.217delT	p.F73fs	.	.	41	4	86	0	.	90
XPO4	64328	bcgsc.ca	37	13	21442811	21442811	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	XPO4	NM_022459	exon2	c.A99G	p.Q33Q	.	.	102	5	72	0	.	272
XRCC4	7518	bcgsc.ca	37	5	82648978	82648978	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	XRCC4	NM_022406	exon8	c.A928G	p.K310E	.	.	300	0	278	3	.	229
XYLT1	64131	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	16	17211555	17211555	+	Silent	SNP	G	G	T	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	XYLT1	NM_022166	exon11	c.C2505A	p.T835T	.	.	216	106	218	0	.	94
ZBED4	9889	bcgsc.ca	37	22	50280277	50280277	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZBED4	NM_014838	exon2	c.2967delG	p.M989fs	.	.	42	4	101	0	.	92
ZC2HC1C	79696	bcgsc.ca	37	14	75538052	75538052	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	NM_024643	exon2	c.776delA	p.E259fs	.	.	44	4	75	0	.	.
ZC3H7A	29066	bcgsc.ca	37	16	11868109	11868109	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZC3H7A	NM_014153	exon9	c.A886G	p.T296A	.	.	155	5	200	0	.	94
ZFP42	132625	broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	188924586	188924586	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZFP42	NM_174900	exon4	c.C625A	p.L209I	.	.	73	21	89	1	.	228
ZMIZ2	83637	hgsc.bcm.edu;broad.mit.edu	37	7	44796547	44796547	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZMIZ2	NM_174929	exon3	c.167delT	p.V56fs	.	.	152	10	166	0	.	137
ZMYM1	79830	bcgsc.ca	37	1	35559634	35559634	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZMYM1	NM_024772	exon2	c.T46C	p.S16P	.	.	85	4	67	0	.	90
ZNF252P	286101	bcgsc.ca	37	8	146202039	146202039	+	RNA	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	12	3	25	0	.	.
ZNF257	113835	bcgsc.ca	37	19	22271975	22271975	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF257	NM_033468	exon4	c.1423delA	p.T475fs	.	.	29	3	72	0	.	90
ZNF564	163050	bcgsc.ca	37	19	12638001	12638001	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF564	NM_144976	exon4	c.A921G	p.G307G	.	.	53	4	80	0	.	91
ZNF697	90874	bcgsc.ca	37	1	120168499	120168499	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF697	NM_001080470	exon2	c.A225G	p.T75T	.	.	80	4	125	0	.	23
ZNF704	619279	bcgsc.ca	37	8	81571849	81571849	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF704	NM_001033723	exon7	c.T1003C	p.S335P	.	.	53	4	106	0	.	90
ZNF780B	163131	bcgsc.ca	37	19	40553304	40553304	+	Silent	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF780B	NM_001005851	exon4	c.A210G	p.K70K	.	.	160	5	198	0	.	47
ZNF781	163115	bcgsc.ca	37	19	38160811	38160811	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	ZNF781	NM_152605	exon4	c.A239G	p.K80R	.	.	73	4	65	0	.	90
SLCO1B7	338821	hgsc.bcm.edu	37	12	21207384	21207385	+	Splice_Site	DNP	AG	AG	CT	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	.	.	.	.	.	.	.	.	
TBC1D9B	23061	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	5	179331759	179331760	+	Missense_Mutation	DNP	GG	GG	AA	novel		TCGA-BC-A3KG-01A-11D-A20W-10	TCGA-BC-A3KG-10A-01D-A20W-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d178885-f113-42a2-b34d-d564960d9314	685e0c81-2971-413a-9a2e-de27a62de591	.	.	.	.	.	p.P58S	.	.	.	.	.	.	.	
