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
ADAM23	8745	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	207437884	207437884	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ADAM23	NM_003812	exon18	c.G1702C	p.D568H	.	.	102	12	165	1	.	228
ADCY3	109	broad.mit.edu;ucsc.edu	37	2	25057765	25057765	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ADCY3	NM_004036	exon9	c.G1703A	p.R568H	.	.	40	7	72	1	.	94
ADH1B	125	bcgsc.ca	37	4	100237413	100237413	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ADH1B	NM_000668	exon4	c.306delA	p.R102fs	.	.	187	117	472	5	.	136
AEBP1	165	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	44151907	44151907	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	AEBP1	NM_001129	exon17	c.C2204T	p.S735L	.	.	52	19	86	1	.	90
ALDH1L1	10840	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	125844550	125844550	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ALDH1L1	NM_001270364	exon15	c.T1739C	p.I580T	.	.	131	19	153	1	.	156
ALG3	10195	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	183963596	183963596	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_005787	exon2	c.A201G	p.T67T	.	.	73	32	76	1	.	.
ALKBH7	84266	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	6374593	6374593	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ALKBH7	NM_032306	exon3	c.A496C	p.I166L	.	.	29	15	69	2	.	90
ALPL	249	ucsc.edu	37	1	21890624	21890624	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ALPL	NM_000478	exon6	c.C563A	p.S188X	.	.	31	4	61	1	.	94
AMMECR1L	83607	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	128628831	128628831	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	AMMECR1L	NM_031445	exon4	c.G510A	p.T170T	.	.	44	10	74	0	.	90
ANKRD55	79722	bcgsc.ca	37	5	55407540	55407540	+	Silent	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ANKRD55	NM_024669	exon10	c.G1035C	p.V345V	.	.	60	32	93	2	.	91
ANTXR1	84168	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	69379336	69379336	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ANTXR1	NM_032208	exon13	c.C987T	p.I329I	.	.	35	19	64	1	.	94
ARHGEF18	23370	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	7535139	7535139	+	Silent	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ARHGEF18	NM_001130955	exon19	c.C3477G	p.L1159L	.	.	51	27	115	1	.	228
ART3	419	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	77025763	77025763	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ART3	NM_001130016	exon10	c.A984G	p.P328P	.	.	47	36	97	1	.	92
ATP13A2	23400	broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	17331296	17331296	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ATP13A2	NM_001141973	exon5	c.C368T	p.S123F	.	.	59	6	125	0	.	93
ATP1A2	477	ucsc.edu;bcgsc.ca	37	1	160106381	160106381	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ATP1A2	NM_000702	exon19	c.G2585T	p.G862V	.	.	87	32	105	2	.	518
ATP2B2	491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	10417206	10417206	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ATP2B2	NM_001001331	exon11	c.A1324G	p.K442E	.	.	126	13	135	0	.	95
BAI3	577	ucsc.edu;bcgsc.ca	37	6	69349266	69349266	+	Missense_Mutation	SNP	G	G	T	rs146475807	alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	BAI3	NM_001704	exon3	c.G699T	p.E233D	.	.	23	15	61	2	G|1.000;A|0.000	1148
BCMO1	53630	broad.mit.edu	37	16	81298305	81298305	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	BCMO1	NM_017429	exon5	c.G532T	p.A178S	.	.	97	3	217	0	.	90
BLOC1S3	388552	bcgsc.ca	37	19	45683101	45683101	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	BLOC1S3	NM_212550	exon2	c.547delC	p.L183fs	.	.	23	6	42	0	.	90
BLOC1S3	388552	bcgsc.ca	37	19	45683103	45683115	+	Frame_Shift_Del	DEL	GCCGGACATCCGC	GCCGGACATCCGC	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	GCCGGACATCCGC	GCCGGACATCCGC	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	BLOC1S3	NM_212550	exon2	c.549_561del	p.183_187del	.	.	23	5	42	0	.	90
BPNT1	10380	ucsc.edu	37	1	220231487	220231487	+	RNA	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	BPNT1	.	.	.	.	.	.	18	1	26	0	.	91
C17orf66	256957	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	34192351	34192351	+	Missense_Mutation	SNP	G	G	A	rs141724302	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	C17orf66	NM_152781	exon3	c.C188T	p.P63L	.	.	96	30	86	0	G|0.994;A|0.006	155
C17orf96	100170841	broad.mit.edu	37	17	36829665	36829665	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_001130677	exon1	c.G1084A	p.A362T	.	.	72	3	70	1	.	.
C6orf222	389384	bcgsc.ca	37	6	36287312	36287312	+	Missense_Mutation	SNP	G	G	C	rs743852	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	C6orf222	NM_001010903	exon11	c.C1744G	p.L582V	.	.	96	5	101	0	G|0.540;C|0.460	93
CAMSAP2	23271	bcgsc.ca	37	1	200801446	200801446	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_203459	exon5	c.G764C	p.C255S	.	.	191	84	273	4	.	.
CCDC144C	348254	broad.mit.edu;ucsc.edu;mdanderson.org	37	17	20224663	20224663	+	RNA	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	.	.	.	48	16	105	0	.	.
CCNJL	79616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	159686508	159686508	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CCNJL	NM_024565	exon5	c.A695C	p.Y232S	.	.	31	7	48	0	.	90
CDC6	990	bcgsc.ca	37	17	38451607	38451607	+	Splice_Site	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CDC6	NM_001254	exon8	c.1084-1G>A	.	.	.	101	57	98	2	.	662
CILP2	148113	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	19655201	19655201	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CILP2	NM_153221	exon8	c.C1847A	p.T616N	.	.	41	17	71	0	.	91
CNTNAP5	129684	bcgsc.ca	37	2	125671729	125671729	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CNTNAP5	NM_130773	exon24	c.T3785C	p.L1262P	.	.	223	88	334	4	.	524
COL22A1	169044	broad.mit.edu	37	8	139674327	139674327	+	Splice_Site	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	COL22A1	NM_152888	exon44	c.3187-1G>T	.	.	.	75	5	49	0	.	103
COL5A2	1290	broad.mit.edu;bcgsc.ca	37	2	190044308	190044308	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	COL5A2	NM_000393	exon1	c.C23A	p.A8E	.	.	64	5	83	0	.	92
COQ10B	80219	bcgsc.ca	37	2	198318367	198318375	+	In_Frame_Del	DEL	AGGCGCCCG	AGGCGCCCG	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	AGGCGCCCG	AGGCGCCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	COQ10B	NM_025147	exon1	c.83_91del	p.28_31del	.	.	111	36	193	3	.	90
CPAMD8	27151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	17040002	17040002	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CPAMD8	NM_015692	exon24	c.A3035T	p.Q1012L	.	.	30	5	37	0	.	141
CSMD1	64478	hgsc.bcm.edu;broad.mit.edu	37	8	3165845	3165845	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CSMD1	NM_033225	exon24	c.C3812A	p.P1271H	.	.	22	4	71	0	.	86
CTNNB1	1499	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	41274909	41274909	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CTNNB1	NM_001098209	exon8	c.A1159T	p.N387Y	.	.	170	64	173	1	.	24361
CTSD	1509	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	11	1778644	1778644	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CTSD	NM_001909	exon5	c.G614A	p.R205H	.	.	68	34	61	0	.	90
CYFIP2	26999	broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	156712348	156712348	+	Splice_Site	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CYFIP2	.	.	.	.	.	.	39	6	39	0	.	22
CYLD	1540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	50815217	50815217	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	CYLD	NM_015247	exon11	c.G1579A	p.A527T	.	.	55	17	105	0	.	2444
DDX19B	11269	broad.mit.edu;bcgsc.ca;mdanderson.org	37	16	70366883	70366883	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	DDX19B	NM_007242	exon11	c.A1199C	p.E400A	.	.	256	36	495	1	.	226
DHTKD1	55526	ucsc.edu;bcgsc.ca	37	10	12131085	12131085	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	DHTKD1	NM_018706	exon5	c.T818G	p.F273C	.	.	53	19	114	2	.	515
DSCAM	1826	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	42080424	42080424	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	DSCAM	NM_001271534	exon2	c.A317T	p.N106I	.	.	46	15	69	0	.	101
EEA1	8411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	93205205	93205205	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EEA1	NM_003566	exon17	c.A2049G	p.L683L	.	.	43	11	48	0	.	229
EPHA6	285220	bcgsc.ca	37	3	96706792	96706792	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EPHA6	NM_001080448	exon3	c.T1069C	p.C357R	.	.	96	54	113	3	.	1561
EYS	346007	broad.mit.edu	37	6	65301075	65301075	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EYS	NM_001142800	exon26	c.C4685A	p.T1562N	.	.	80	4	146	0	.	660
EYS	346007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	65612320	65612320	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	EYS	NM_001142800	exon17	c.T2715C	p.C905C	.	.	121	26	203	0	.	660
FAM5C	339479	ucsc.edu;bcgsc.ca	37	1	190423871	190423871	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FAM5C	NM_199051	exon2	c.T150A	p.D50E	.	.	119	22	156	2	.	228
FAM78A	286336	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	134136583	134136583	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FAM78A	NM_033387	exon2	c.G478A	p.D160N	.	.	30	7	57	0	.	91
FASN	2194	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	80051623	80051623	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FASN	NM_004104	exon4	c.G305A	p.G102E	.	.	68	40	45	0	.	90
FBXW8	26259	hgsc.bcm.edu	37	12	117349014	117349014	+	Missense_Mutation	SNP	C	C	G	rs11068230		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FBXW8	NM_153348	exon1	c.C172G	p.R58G	.	.	6	6	0	0	C|0.233;G|0.767	229
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	4	1807577	1807577	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FGFR3	NM_001163213	exon13	c.C1752T	p.C584C	.	.	54	16	76	0	.	9542
FHDC1	85462	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	4	153896514	153896514	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FHDC1	NM_033393	exon11	c.G2071T	p.E691X	.	.	29	12	71	0	.	136
FMN2	56776	broad.mit.edu	37	1	240256396	240256396	+	Silent	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FMN2	NM_020066	exon1	c.G987C	p.G329G	.	.	6	3	14	0	.	145
FOS	2353	broad.mit.edu;mdanderson.org	37	14	75747795	75747795	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	FOS	NM_005252	exon4	c.G811A	p.D271N	.	.	13	6	20	1	.	847
GLRA4	441509	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	102978843	102978843	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GLRA4	NM_001024452	exon5	c.T518G	p.L173R	.	.	102	69	280	1	.	108
GPR158	57512	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	25464385	25464385	+	Silent	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GPR158	NM_020752	exon1	c.C36A	p.L12L	.	.	57	19	61	1	.	141
GPR98	84059	ucsc.edu	37	5	89925241	89925241	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GPR98	NM_032119	exon9	c.T1724A	p.L575X	.	.	106	52	176	3	.	103
GRIN3A	116443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	104499796	104499796	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GRIN3A	NM_133445	exon1	c.G466C	p.A156P	.	.	54	19	108	0	.	96
GRM7	2917	bcgsc.ca	37	3	7348271	7348271	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GRM7	NM_000844	exon4	c.C965A	p.P322Q	.	.	136	70	208	5	.	526
GRXCR1	389207	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	42895456	42895456	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	GRXCR1	NM_001080476	exon1	c.C173A	p.S58Y	.	.	91	58	134	1	.	23
HERC6	55008	bcgsc.ca	37	4	89318063	89318063	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HERC6	NM_017912	exon7	c.A948G	p.P316P	.	.	45	27	127	4	.	658
HGS	9146	hgsc.bcm.edu;broad.mit.edu	37	17	79660939	79660939	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HGS	NM_004712	exon11	c.880delC	p.P294fs	.	.	54	15	28	0	.	91
HIST1H1D	3007	bcgsc.ca	37	6	26235093	26235093	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HIST1H1D	NM_005320	exon1	c.G69A	p.K23K	.	.	64	55	138	3	.	91
HNRNPUL1	11100	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	41785002	41785002	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HNRNPUL1	NM_007040	exon6	c.G807A	p.V269V	.	.	39	14	64	1	.	69
HSD11B1	3290	bcgsc.ca	37	1	209880365	209880365	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	HSD11B1	NM_001206741	exon5	c.C409T	p.R137C	.	.	72	37	101	3	.	153
IL17RE	132014	broad.mit.edu	37	3	9953248	9953248	+	Silent	SNP	C	C	T	rs150541120	byfrequency;alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	IL17RE	NM_153483	exon13	c.C1314T	p.D438D	.	.	69	12	92	2	C|0.999;A|0.001	90
IL5RA	3568	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	3137002	3137002	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	IL5RA	NM_001243099	exon8	c.C836A	p.T279K	.	.	116	51	161	0	.	91
IL9R	3581	broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	155233210	155233210	+	Missense_Mutation	SNP	G	G	T	rs182426355	by1000genomes;alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	IL9R	NM_176786	exon4	c.G380T	p.W127L	.	.	76	37	150	1	G|1.000;A|0.000	40
INSRR	3645	hgsc.bcm.edu	37	1	156815550	156815550	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	INSRR	NM_014215	exon10	c.C2035A	p.P679T	.	.	81	4	76	0	.	1403
IQCE	23288	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	2625881	2625881	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	IQCE	NM_152558	exon12	c.G864A	p.K288K	.	.	45	9	61	1	.	226
ITIH6	347365	mdanderson.org	37	X	54783516	54783516	+	Silent	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_198510	exon8	c.C2991A	p.I997I	.	.	18	3	36	0	.	.
JAKMIP1	152789	bcgsc.ca	37	4	6027982	6027982	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	JAKMIP1	NM_001099433	exon21	c.C2469T	p.F823F	.	.	202	100	496	4	.	292
KALRN	8997	broad.mit.edu	37	3	124385368	124385368	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KALRN	NM_001024660	exon46	c.C6415T	p.Q2139X	.	.	66	5	95	0	.	738
KAT6B	23522	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	76789864	76789864	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_012330	exon18	c.G5282A	p.S1761N	.	.	31	12	57	1	.	.
KCNA5	3741	broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	5154790	5154790	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KCNA5	NM_002234	exon1	c.G1477A	p.G493S	.	.	67	28	112	2	.	715
KCNH4	23415	broad.mit.edu	37	17	40328103	40328103	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KCNH4	NM_012285	exon5	c.C798T	p.S266S	.	.	98	4	90	0	.	153
KLRF1	51348	ucsc.edu;bcgsc.ca	37	12	9997089	9997089	+	Silent	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KLRF1	NM_016523	exon6	c.C663A	p.T221T	.	.	117	50	186	3	.	135
KRT4	3851	bcgsc.ca	37	12	53207603	53207603	+	Silent	SNP	A	A	G	rs7135148	bycluster;by2hit2allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRT4	NM_002272	exon1	c.T240C	p.F80F	.	.	54	13	56	0	A|1.000;|0.000	96
KRT4	3851	bcgsc.ca	37	12	53207606	53207606	+	Silent	SNP	G	G	A	rs79164931	bycluster;by1000genomes	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRT4	NM_002272	exon1	c.C237T	p.G79G	.	.	53	13	57	0	.	96
KRT6C	286887	ucsc.edu;bcgsc.ca	37	12	52865932	52865932	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRT6C	NM_173086	exon2	c.C673A	p.L225M	.	.	151	62	207	3	.	114
KRT8	3856	broad.mit.edu	37	12	53298675	53298675	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRT8	NM_001256282	exon2	c.T175G	p.S59A	.	.	58	8	80	1	.	92
KRTAP4-8	728224	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	39254310	39254310	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_031960	exon1	c.G27A	p.V9V	.	.	165	26	192	1	.	.
KRTAP5-5	439915	bcgsc.ca	37	11	1651199	1651199	+	Silent	SNP	A	A	G	rs144216147		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRTAP5-5	NM_001001480	exon1	c.A129G	p.G43G	.	.	78	40	93	14	.	23
KRTAP5-5	439915	bcgsc.ca	37	11	1651211	1651211	+	Silent	SNP	C	C	A	rs190828070	by1000genomes	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KRTAP5-5	NM_001001480	exon1	c.C141A	p.G47G	.	.	72	24	104	2	C|0.932;A|0.068	23
KSR2	283455	broad.mit.edu	37	12	117909020	117909020	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	KSR2	NM_173598	exon18	c.G2601C	p.Q867H	.	.	69	3	109	0	.	1449
LAMA1	284217	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	7002349	7002349	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LAMA1	NM_005559	exon30	c.T4296C	p.D1432D	.	.	37	9	52	0	.	149
LAMA1	284217	ucsc.edu;bcgsc.ca	37	18	6958596	6958596	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LAMA1	NM_005559	exon55	c.G7844A	p.S2615N	.	.	125	24	206	2	.	149
LOC642236	0	bcgsc.ca	37	9	68433510	68433510	+	RNA	SNP	C	C	G	rs75661796	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	.	.	.	243	12	430	9	C|0.583;G|0.417	.
LOC646762	0	broad.mit.edu	37	7	29690891	29690891	+	RNA	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	.	.	.	9	4	15	0	.	.
LRP2	4036	ucsc.edu;bcgsc.ca	37	2	170062623	170062623	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LRP2	NM_004525	exon40	c.T7466A	p.M2489K	.	.	128	49	188	4	.	175
LRRC17	10234	ucsc.edu;bcgsc.ca	37	7	102584837	102584837	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LRRC17	NM_001031692	exon4	c.A1109G	p.N370S	.	.	180	101	225	3	.	91
LY6H	4062	broad.mit.edu	37	8	144240263	144240263	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	LY6H	NM_001135655	exon3	c.C207T	p.S69S	.	.	124	10	73	1	.	90
MAP3K1	4214	hgsc.bcm.edu	37	5	56111751	56111751	+	Silent	SNP	G	G	C	rs28710284	bycluster;byfrequency;by1000genomes	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MAP3K1	NM_005921	exon1	c.G351C	p.A117A	.	.	6	6	0	0	G|0.348;C|0.652	956
MAP4K5	11183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	50911780	50911780	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MAP4K5	NM_006575	exon18	c.G1318T	p.V440L	.	.	73	16	122	0	.	546
MGAM	8972	broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	141755415	141755415	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MGAM	NM_004668	exon28	c.C3372T	p.T1124T	.	.	72	14	93	1	.	70
MSN	4478	bcgsc.ca	37	X	64951035	64951044	+	Frame_Shift_Del	DEL	ACACCGTGGC	ACACCGTGGC	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	ACACCGTGGC	ACACCGTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MSN	NM_002444	exon5	c.534_543del	p.178_181del	.	.	61	22	163	1	.	1086
MTMR7	9108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	17163407	17163407	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MTMR7	NM_004686	exon11	c.A1211C	p.E404A	.	.	33	14	142	0	.	91
MYO9B	4650	ucsc.edu;bcgsc.ca;mdanderson.org	37	19	17283665	17283665	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	MYO9B	NM_001130065	exon13	c.A2033G	p.D678G	.	.	16	7	44	2	.	67
NBPF10	100132406	broad.mit.edu	37	1	145299792	145299792	+	Missense_Mutation	SNP	A	A	G	rs61814628		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_001039703	exon6	c.A841G	p.S281G	.	.	58	6	95	2	.	.
NEB	4703	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	152476269	152476269	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NEB	NM_001271208	exon73	c.A10568G	p.Y3523C	.	.	76	28	132	1	.	145
NFXL1	152518	ucsc.edu;bcgsc.ca	37	4	47900847	47900847	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NFXL1	NM_152995	exon8	c.G1016C	p.S339T	.	.	128	63	243	3	.	524
NLRX1	79671	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	119052990	119052990	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NLRX1	NM_024618	exon9	c.G2542A	p.G848S	.	.	25	7	56	0	.	92
NOMO1	23420	bcgsc.ca	37	16	14970644	14970644	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NOMO1	NM_014287	exon22	c.T2640A	p.F880L	.	.	431	101	742	7	.	45
NOVA2	4858	bcgsc.ca	37	19	46443198	46443198	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NOVA2	NM_002516	exon4	c.G1402T	p.A468S	.	.	70	31	110	3	.	226
NR4A3	8013	hgsc.bcm.edu	37	9	102591042	102591042	+	Missense_Mutation	SNP	A	A	G	rs12344570	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NR4A3	NM_173200	exon4	c.A751G	p.S251G	.	.	4	4	0	0	A|0.569;G|0.431	186
NRXN2	9379	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	64434901	64434901	+	Missense_Mutation	SNP	C	C	A	rs143130600	alternate_allele	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	NRXN2	NM_015080	exon9	c.G1619T	p.G540V	.	.	49	11	81	0	C|1.000;T|0.000	232
OBSCN	84033	ucsc.edu;bcgsc.ca	37	1	228451857	228451857	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OBSCN	NM_001271223	exon18	c.G5178T	p.R1726S	.	.	157	57	210	2	.	403
OR13A1	79290	ucsc.edu;bcgsc.ca	37	10	45799736	45799736	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR13A1	NM_001004297	exon4	c.A135G	p.L45L	.	.	129	33	157	3	.	68
OR2M7	391196	ucsc.edu;bcgsc.ca	37	1	248487600	248487600	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR2M7	NM_001004691	exon1	c.T271C	p.S91P	.	.	163	76	206	2	.	70
OR2T10	127069	bcgsc.ca	37	1	248756641	248756641	+	Silent	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR2T10	NM_001004693	exon1	c.C429A	p.L143L	.	.	160	66	242	6	.	69
OR2T27	403239	bcgsc.ca	37	1	248813271	248813271	+	Silent	SNP	C	C	A	rs2802081	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR2T27	NM_001001824	exon1	c.G915T	p.V305V	.	.	193	12	228	7	C|0.968;A|0.032	47
OR52N4	390072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	5776243	5776243	+	Silent	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR52N4	NM_001005175	exon1	c.C273G	p.L91L	.	.	74	12	123	0	.	2
OR7D2	162998	broad.mit.edu;mdanderson.org	37	19	9296842	9296842	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	OR7D2	NM_175883	exon1	c.C385A	p.P129T	.	.	18	3	75	0	.	71
P2RY1	5028	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	152553754	152553754	+	Silent	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	P2RY1	NM_002563	exon1	c.A183G	p.V61V	.	.	159	17	209	1	.	500
PABPC5	140886	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	90690699	90690699	+	Silent	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PABPC5	NM_080832	exon2	c.T123A	p.A41A	.	.	16	10	53	0	.	110
PAX6	5080	ucsc.edu;bcgsc.ca	37	11	31815289	31815289	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PAX6	NM_001604	exon11	c.G869T	p.R290I	.	.	134	53	160	2	.	1086
PDE4A	5141	bcgsc.ca	37	19	10531608	10531608	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PDE4A	NM_001111307	exon1	c.G168T	p.E56D	.	.	23	12	32	1	.	523
PIH1D2	120379	bcgsc.ca	37	11	111941897	111941897	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PIH1D2	NM_001082619	exon4	c.G412A	p.E138K	.	.	75	15	150	3	.	69
PIK3CG	5294	bcgsc.ca	37	7	106508945	106508945	+	Silent	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PIK3CG	NM_002649	exon2	c.G939T	p.P313P	.	.	24	13	64	2	.	1316
PIK3R1	5295	broad.mit.edu	37	5	67569772	67569772	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PIK3R1	NM_181523	exon4	c.G433C	p.E145Q	.	.	43	5	89	1	.	4332
PITPNC1	26207	bcgsc.ca	37	17	65665772	65665772	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PITPNC1	NM_012417	exon7	c.T611A	p.V204E	.	.	71	44	102	3	.	226
PKP1	5317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	201294914	201294914	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PKP1	NM_000299	exon13	c.T2117C	p.L706P	.	.	116	25	139	0	.	92
PLAA	9373	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	26905887	26905887	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PLAA	NM_001031689	exon14	c.G2010C	p.Q670H	.	.	93	22	198	0	.	514
PLD1	5337	bcgsc.ca	37	3	171362704	171362704	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PLD1	NM_002662	exon22	c.T2539C	p.Y847H	.	.	81	39	106	3	.	660
POLA1	5422	bcgsc.ca	37	X	24735441	24735441	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	POLA1	NM_016937	exon9	c.G723A	p.E241E	.	.	49	33	117	3	.	229
PORCN	64840	broad.mit.edu;bcgsc.ca;mdanderson.org	37	X	48375573	48375573	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PORCN	NM_203475	exon13	c.C1176T	p.G392G	.	.	10	8	50	1	.	133
POU2F1	5451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	167384897	167384897	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	POU2F1	NM_002697	exon16	c.T2151C	p.S717S	.	.	80	21	133	0	.	579
PRKACB	5567	ucsc.edu;bcgsc.ca	37	1	84647892	84647892	+	Missense_Mutation	SNP	G	G	A	rs148797911		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PRKACB	NM_182948	exon3	c.G259A	p.G87R	.	.	87	18	174	3	G|1.000;A|0.000	1083
PRMT1	3276	broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	50180570	50180570	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PRMT1	NM_001207042	exon1	c.G33A	p.M11I	.	.	18	4	31	0	.	91
PRPF8	10594	broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	1576479	1576479	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PRPF8	NM_006445	exon24	c.C3670T	p.R1224C	.	.	21	15	63	1	.	525
PRR12	57479	broad.mit.edu	37	19	50102767	50102767	+	Missense_Mutation	SNP	C	C	T	rs201161028		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PRR12	NM_020719	exon5	c.C3917T	p.P1306L	.	.	49	3	51	0	.	70
PRSS41	360226	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	2854526	2854526	+	Silent	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_001135086	exon4	c.T717C	p.D239D	.	.	53	10	75	0	.	.
PTCD3	55037	ucsc.edu;bcgsc.ca	37	2	86338249	86338249	+	Missense_Mutation	SNP	G	G	A	rs78436829	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PTCD3	NM_017952	exon4	c.G208A	p.V70I	.	.	117	37	189	3	G|0.997;A|0.003	91
PTOV1	53635	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	50361895	50361895	+	Silent	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PTOV1	NM_017432	exon10	c.C1026A	p.I342I	.	.	52	25	81	0	.	226
PTPRA	5786	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	2988018	2988018	+	Silent	SNP	G	G	A	rs142755718		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PTPRA	NM_002836	exon15	c.G858A	p.P286P	.	.	106	14	106	0	G|1.000;A|0.000	227
PTPRC	5788	ucsc.edu;bcgsc.ca	37	1	198721765	198721765	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PTPRC	NM_002838	exon31	c.T3373A	p.W1125R	.	.	111	27	158	2	.	295
PXK	54899	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	58395296	58395296	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	PXK	NM_017771	exon15	c.A1346G	p.H449R	.	.	196	92	253	1	.	334
RAB9B	51209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	103080318	103080318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RAB9B	NM_016370	exon3	c.G397A	p.V133M	.	.	24	17	91	0	.	659
RBFOX2	23543	hgsc.bcm.edu	37	22	36424450	36424450	+	Missense_Mutation	SNP	A	A	C	rs9607299	bycluster;byfrequency;by1000genomes	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RBFOX2	NM_001082579	exon1	c.T24G	p.H8Q	.	.	7	7	0	0	A|0.014;C|0.986	90
RBM42	79171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	36120133	36120133	+	Silent	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RBM42	NM_024321	exon1	c.G78T	p.P26P	.	.	27	11	35	0	.	90
RBP3	5949	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	48389747	48389747	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RBP3	NM_002900	exon1	c.G1131A	p.Q377Q	.	.	41	15	57	0	.	153
RET	5979	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	43600449	43600449	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RET	NM_020975	exon4	c.G675A	p.T225T	.	.	40	13	59	0	.	4507
RFX3	5991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	3247979	3247979	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RFX3	NM_002919	exon16	c.A2021T	p.E674V	.	.	32	12	66	0	.	93
RRS1	23212	broad.mit.edu	37	8	67341932	67341932	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RRS1	NM_015169	exon1	c.G566T	p.R189L	.	.	128	3	100	0	.	90
RTKN2	219790	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	63957724	63957724	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RTKN2	NM_145307	exon12	c.G1773T	p.R591S	.	.	104	37	173	2	.	68
RXRG	6258	ucsc.edu;bcgsc.ca	37	1	165398166	165398166	+	Silent	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	RXRG	NM_006917	exon2	c.A87T	p.P29P	.	.	72	31	76	2	.	186
SEPT7P2	641977	broad.mit.edu	37	7	45786858	45786858	+	RNA	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	.	.	.	75	13	94	0	.	.
SERPINA6	866	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	94772500	94772500	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SERPINA6	NM_001756	exon4	c.G940T	p.D314Y	.	.	78	30	118	1	.	653
SH3BP2	6452	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	2829348	2829348	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SH3BP2	NM_001145856	exon7	c.A704G	p.D235G	.	.	67	30	127	0	.	514
SHROOM4	57477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	50350826	50350826	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SHROOM4	NM_020717	exon6	c.C3316A	p.P1106T	.	.	30	17	92	0	.	131
SIK1	150094	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	44841639	44841639	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SIK1	NM_173354	exon5	c.G378A	p.A126A	.	.	78	24	111	0	.	346
SLC35G6	643664	ucsc.edu	37	17	7386234	7386234	+	Missense_Mutation	SNP	G	G	A	rs200251320	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_001102614	exon2	c.G931A	p.V311M	.	.	29	5	93	6	G|0.793;A|0.207	.
SLC5A5	6528	ucsc.edu;bcgsc.ca	37	19	18004537	18004537	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SLC5A5	NM_000453	exon15	c.C1783T	p.P595S	.	.	96	35	137	2	.	93
SNF8	11267	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	47014463	47014463	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SNF8	NM_007241	exon4	c.A268T	p.M90L	.	.	124	32	135	2	.	90
SORBS1	10580	broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	97101323	97101323	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SORBS1	NM_001034955	exon25	c.G2608A	p.E870K	.	.	61	25	86	1	.	155
SPECC1	92521	ucsc.edu;bcgsc.ca	37	17	20107972	20107972	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SPECC1	NM_001033553	exon4	c.G610T	p.G204W	.	.	81	60	204	2	.	639
SPEG	10290	bcgsc.ca	37	2	220349004	220349004	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SPEG	NM_005876	exon30	c.G6819A	p.K2273K	.	.	52	18	99	2	.	383
STIP1	10963	broad.mit.edu;bcgsc.ca	37	11	63964989	63964989	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	STIP1	NM_006819	exon7	c.A824G	p.Y275C	.	.	66	13	104	2	.	93
STK4	6789	broad.mit.edu	37	20	43625882	43625882	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	STK4	NM_006282	exon7	c.G766T	p.D256Y	.	.	291	6	346	0	.	767
SUN5	140732	bcgsc.ca	37	20	31577506	31577506	+	Splice_Site	DEL	T	T	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SUN5	NM_080675	exon10	c.535-2A>-	.	.	.	66	21	80	1	.	91
SVEP1	79987	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	113312149	113312149	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SVEP1	NM_153366	exon2	c.C767G	p.A256G	.	.	83	16	171	0	.	75
SYNDIG1	79953	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	24565510	24565510	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SYNDIG1	NM_024893	exon3	c.A499G	p.T167A	.	.	64	29	60	1	.	91
SYNE2	23224	ucsc.edu;bcgsc.ca	37	14	64518505	64518505	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	SYNE2	NM_182914	exon48	c.A7874T	p.Y2625F	.	.	225	87	331	2	.	164
TAF1C	9013	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	84214736	84214736	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TAF1C	NM_005679	exon11	c.G1299T	p.Q433H	.	.	54	28	114	0	.	91
TBC1D10B	26000	broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	30370140	30370140	+	Splice_Site	SNP	T	T	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_015527	exon9	c.1643-2A>T	.	.	.	56	16	83	1	.	.
TEK	7010	broad.mit.edu;ucsc.edu	37	9	27212818	27212818	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TEK	NM_000459	exon17	c.T2800C	p.S934P	.	.	23	6	55	1	.	1584
TEP1	7011	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	20874511	20874511	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TEP1	NM_007110	exon3	c.C616T	p.P206S	.	.	29	7	48	1	.	95
TMEM38B	55151	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	9	108536210	108536210	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TMEM38B	NM_018112	exon6	c.G725A	p.W242X	.	.	95	34	158	0	.	92
TMPRSS11E	28983	bcgsc.ca	37	4	69327622	69327622	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_1	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TMPRSS11E	NM_014058	exon2	c.T95C	p.L32P	.	.	264	167	605	10	.	70
TOR4A	54863	broad.mit.edu	37	9	140173601	140173601	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_017723	exon2	c.G460A	p.E154K	.	.	33	10	43	2	.	.
TP53	7157	hgsc.bcm.edu;bcgsc.ca	37	17	7579389	7579399	+	Frame_Shift_Del	DEL	GGGAAGGGACA	GGGAAGGGACA	-	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	GGGAAGGGACA	GGGAAGGGACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	TP53,head_neck,carcinoma,0	TP53	NM_000546	exon4	c.288_298del	p.96_100del	.	.	65	23	195	0	.	70225
TUBGCP2	10844	ucsc.edu;bcgsc.ca	37	10	135113524	135113524	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	TUBGCP2	NM_001256617	exon3	c.G244A	p.V82M	.	.	115	52	124	2	.	90
UBXN1	51035	ucsc.edu;mdanderson.org	37	11	62445985	62445985	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	UBXN1	NM_015853	exon3	c.G202T	p.E68X	.	.	59	11	124	2	.	90
ULK4	54986	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	41954356	41954356	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ULK4	NM_017886	exon9	c.G839C	p.W280S	.	.	76	25	119	2	.	297
UNKL	64718	ucsc.edu;bcgsc.ca	37	16	1417119	1417119	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	UNKL	NM_023076	exon5	c.C517T	p.R173C	.	.	44	4	64	0	.	90
URB2	9816	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	229770867	229770867	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	URB2	NM_014777	exon4	c.G507T	p.L169F	.	.	81	27	104	1	.	174
USH2A	7399	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	215802343	215802343	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	USH2A	NM_206933	exon71	c.C15332T	p.T5111I	.	.	109	13	164	0	.	115
VWDE	221806	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	12409323	12409323	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	VWDE	NM_001135924	exon12	c.G2609T	p.G870V	.	.	116	37	167	1	.	68
WDFY4	57705	broad.mit.edu;mdanderson.org	37	10	50022037	50022037	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	WDFY4	NM_020945	exon31	c.G5250A	p.Q1750Q	.	.	16	4	37	0	.	22
WDR91	29062	broad.mit.edu;bcgsc.ca	37	7	134894445	134894445	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	WDR91	NM_014149	exon2	c.G186A	p.R62R	.	.	53	23	102	2	.	137
ZBTB32	27033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	36207170	36207170	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZBTB32	NM_014383	exon5	c.A1160T	p.Q387L	.	.	81	27	82	0	.	92
ZFHX4	79776	ucsc.edu;bcgsc.ca	37	8	77775784	77775784	+	Silent	SNP	C	C	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZFHX4	NM_024721	exon11	c.C9834T	p.L3278L	.	.	152	51	119	3	.	98
ZFP42	132625	ucsc.edu;bcgsc.ca	37	4	188924048	188924048	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZFP42	NM_174900	exon4	c.A87T	p.Q29H	.	.	72	48	190	3	.	228
ZNF415	55786	ucsc.edu;bcgsc.ca	37	19	53612923	53612923	+	Silent	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZNF415	NM_018355	exon4	c.C375T	p.R125R	.	.	146	53	224	3	.	91
ZNF525	170958	broad.mit.edu	37	19	53884412	53884412	+	RNA	SNP	G	G	A	rs4438413	byfrequency	TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	.	.	.	131	4	212	1	G|0.470;A|0.530	.
ZNF845	91664	ucsc.edu;bcgsc.ca	37	19	53854400	53854400	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	NM_138374	exon4	c.G472T	p.G158W	.	.	199	78	289	2	.	.
ZNF85	7639	broad.mit.edu;ucsc.edu	37	19	21132332	21132332	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZNF85	NM_001256171	exon5	c.G1102T	p.G368X	.	.	47	12	87	1	.	514
ZNF85	7639	ucsc.edu;bcgsc.ca	37	19	21132585	21132585	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	ZNF85	NM_001256171	exon5	c.G1355A	p.G452E	.	.	79	22	123	2	.	514
C15orf55	256646	ucsc.edu;bcgsc.ca	37	15	34642906	34642907	+	Missense_Mutation	DNP	CC	CC	AA	novel		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	.	.	.	.	.	p.P271K	.	.	.	.	.	.	.	
