Supplementary table S4.4,,,,,,,,,,,,,,,,,,,,
Gene Name,Breast Cancer Driver,Effect,Severity,Genomic Location,Ref,Alt,Amino Acid,cDNA Location,Alt Tumour,VAF Tumour,Tumour Depth,Alt Normal,VAF Normal,Normal Depth,Functional Class,All Mutation Changes,dbSNP,COSMIC,COSMIC IDs,CGC
ABCA6,,SYNONYMOUS_CODING,LOW,17:67079142,G,T,p.Ser1496Ser,c.4488G>T,10,0.092,109,0,0,148,SILENT,p.Ser1496Ser/c.4488G>T,.,NA,NA,NA
AKAP1,,NON_SYNONYMOUS_CODING,MODERATE,17:55196401,A,T,p.Asp110Val,c.329A>T,22,0.198,111,0,0,177,MISSENSE,p.Asp110Val/c.329A>T:p.Asp167Val/c.500A>T:p.Asp878Val/c.2633A>T,.,NA,NA,NA
ARHGEF4,,NON_SYNONYMOUS_CODING,MODERATE,2:131674478,C,T,p.His657Tyr,c.1969C>T,37,0.123,300,0,0,255,MISSENSE,p.His657Tyr/c.1969C>T,rs200864835,NA,NA,NA
BCR,,NON_SYNONYMOUS_CODING,MODERATE,22:23523576,C,G,p.Asp143Glu,c.429C>G,13,0.102,128,0,0,60,MISSENSE,p.Asp143Glu/c.429C>G,.,NA,NA,Y
C15orf32,,NON_SYNONYMOUS_CODING,MODERATE,15:93015676,A,G,p.Thr100Ala,c.298A>G,19,0.117,163,0,0,194,MISSENSE,p.Thr100Ala/c.298A>G,.,NA,NA,NA
C15orf39,,NON_SYNONYMOUS_CODING,MODERATE,15:75500157,G,T,p.Ala458Ser,c.1372G>T,14,0.093,151,0,0,158,MISSENSE,p.Ala458Ser/c.1372G>T:p.Ala590Ser/c.1768G>T,.,NA,NA,NA
C6orf132,,SYNONYMOUS_CODING,LOW,6:42074237,C,G,p.Arg471Arg,c.1413C>G,14,0.119,118,0,0,102,SILENT,p.Arg471Arg/c.1413C>G,.,NA,NA,NA
C9orf3,,SYNONYMOUS_CODING,LOW,9:97717528,G,A,p.Pro301Pro,c.903G>A,26,0.119,218,0,0,291,SILENT,p.Pro301Pro/c.903G>A:p.Pro359Pro/c.1077G>A:p.Pro478Pro/c.1434G>A:p.Pro577Pro/c.1731G>A,.,NA,NA,NA
CEACAM4,,NON_SYNONYMOUS_CODING,MODERATE,19:42132235,G,A,p.Ala55Val,c.164G>A,18,0.135,133,0,0,138,MISSENSE,p.Ala55Val/c.164G>A,.,NA,NA,NA
CHEK1,,SYNONYMOUS_CODING,LOW,11:125495709,A,G,p.Lys18Lys,c.54A>G,12,0.067,178,0,0,92,SILENT,p.Lys18Lys/c.54A>G,.,NA,NA,NA
CHRM3,,NON_SYNONYMOUS_CODING,MODERATE,1:240071724,G,A,p.Glu325Lys,c.973G>A,23,0.114,201,0,0,202,MISSENSE,p.Glu325Lys/c.973G>A,rs201132730,533742,533742,NA
CTNNB1,,SYNONYMOUS_CODING,LOW,3:41275322,G,A,p.Lys489Lys,c.1467G>A,29,0.154,188,0,0,232,SILENT,p.Lys489Lys/c.1467G>A:p.Lys496Lys/c.1488G>A,.,NA,NA,Y
DBP,,NON_SYNONYMOUS_CODING,MODERATE,19:49134207,A,T,p.Phe289Ile,c.865A>T,23,0.132,174,0,0,134,MISSENSE,p.Phe289Ile/c.865A>T,.,NA,NA,NA
DNAAF2,,STOP_GAINED,HIGH,14:50100351,G,C,p.Ser506*,c.1517G>C,24,0.141,170,0,0,158,NONSENSE,p.Ser506*/c.1517G>C,.,NA,NA,NA
DPP9,,SYNONYMOUS_CODING,LOW,19:4697586,G,C,p.Ala384Ala,c.1152G>C,43,0.107,403,1,0.002,401,SILENT,p.Ala384Ala/c.1152G>C,rs376634899,NA,NA,NA
DYSF,,NON_SYNONYMOUS_CODING,MODERATE,2:71742813,A,G,p.Lys242Glu,c.724A>G,19,0.122,156,0,0,163,MISSENSE,p.Lys242Glu/c.724A>G:p.Lys243Glu/c.727A>G:p.Lys273Glu/c.817A>G:p.Lys274Glu/c.820A>G,.,NA,NA,NA
EFCAB4A,,NON_SYNONYMOUS_CODING,MODERATE,11:830323,C,A,p.Arg227Ser,c.679C>A,10,0.075,134,0,0,66,MISSENSE,p.Arg227Ser/c.679C>A,.,NA,NA,NA
EHMT2,,NON_SYNONYMOUS_CODING,MODERATE,6:31850542,C,T,p.Arg1010Gln,c.3029C>T,18,0.1,180,0,0,175,MISSENSE,p.Arg1010Gln/c.3029C>T:p.Arg1044Gln/c.3131C>T:p.Arg1067Gln/c.3200C>T:p.Arg1101Gln/c.3302C>T,.,NA,NA,NA
EIF4G1,,NON_SYNONYMOUS_CODING,MODERATE,3:184045691,C,G,p.Ser1089Cys,c.3266C>G,20,0.076,264,0,0,302,MISSENSE,p.Ser1089Cys/c.3266C>G:p.Ser1090Cys/c.3269C>G:p.Ser1121Cys/c.3362C>G:p.Ser1122Cys/c.3365C>G:p.Ser1198Cys/c.3593C>G:p.Ser1199Cys/c.3596C>G:p.Ser1245Cys/c.3734C>G:p.Ser1246Cys/c.3737C>G:p.Ser1285Cys/c.3854C>G:p.Ser1286Cys/c.3857C>G:p.Ser1292Cys/c.3875C>G,.,NA,NA,NA
EXD3,,NON_SYNONYMOUS_CODING,MODERATE,9:140289783,G,C,p.Asp9Glu,c.27G>C,30,0.096,313,0,0,273,MISSENSE,p.Asp9Glu/c.27G>C,.,NA,NA,NA
FAM190B,,NON_SYNONYMOUS_CODING,MODERATE,10:86132110,G,A,p.Met434Ile,c.1302G>A,19,0.221,86,0,0,123,MISSENSE,p.Met434Ile/c.1302G>A,.,NA,NA,NA
FNDC7,,SYNONYMOUS_CODING,LOW,1:109260451,C,T,p.Ile45Ile,c.135C>T,34,0.193,176,0,0,222,SILENT,p.Ile45Ile/c.135C>T:p.Ile46Ile/c.138C>T,.,NA,NA,NA
FUK,,NON_SYNONYMOUS_CODING,MODERATE,16:70508544,C,T,p.Pro192Leu,c.575C>T,15,0.156,96,1,0.008,120,MISSENSE,p.Pro192Leu/c.575C>T:p.Pro701Leu/c.2102C>T:p.Pro733Leu/c.2198C>T,rs17883716,NA,NA,NA
FUT2,,NON_SYNONYMOUS_CODING,MODERATE,19:49207034,A,C,p.Asp274Ala,c.821A>C,14,0.059,239,0,0,234,MISSENSE,p.Asp274Ala/c.821A>C,.,NA,NA,NA
GAL3ST3,,NON_SYNONYMOUS_CODING,MODERATE,11:65810838,C,T,p.Val146Ile,c.436C>T,27,0.087,309,1,0.005,197,MISSENSE,p.Val146Ile/c.436C>T,.,NA,NA,NA
HECTD1,,NON_SYNONYMOUS_CODING,MODERATE,14:31618175,C,T,p.Glu257Lys,c.769C>T,12,0.162,74,0,0,82,MISSENSE,p.Glu257Lys/c.769C>T:p.Glu783Lys/c.2347C>T,.,NA,NA,NA
HMGCLL1,,SYNONYMOUS_CODING,LOW,6:55304304,A,G,p.Tyr117Tyr,c.351A>G,14,0.131,107,0,0,118,SILENT,p.Tyr117Tyr/c.351A>G:p.Tyr180Tyr/c.540A>G:p.Tyr251Tyr/c.753A>G:p.Tyr283Tyr/c.849A>G:p.Tyr313Tyr/c.939A>G,.,NA,NA,NA
KIF21B,,NON_SYNONYMOUS_CODING,MODERATE,1:200959814,T,A,p.Ser909Cys,c.2725T>A,20,0.104,193,0,0,168,MISSENSE,p.Ser909Cys/c.2725T>A,.,NA,NA,NA
LINGO2,,SYNONYMOUS_CODING,LOW,9:27949038,A,G,p.Ser544Ser,c.1632A>G,22,0.129,170,0,0,195,SILENT,p.Ser544Ser/c.1632A>G,.,NA,NA,NA
LRP5,,SYNONYMOUS_CODING,LOW,11:68157409,G,T,p.Gly491Gly,c.1473G>T,13,0.079,165,0,0,170,SILENT,p.Gly491Gly/c.1473G>T,.,NA,NA,NA
MCAM,,NON_SYNONYMOUS_CODING,MODERATE,11:119182241,G,A,p.Thr418Met,c.1253G>A,31,0.132,235,1,0.004,233,MISSENSE,p.Thr418Met/c.1253G>A:p.Thr469Met/c.1406G>A,rs370712443,NA,NA,NA
MED16,,SYNONYMOUS_CODING,LOW,19:886163,G,C,p.Val162Val,c.486G>C,21,0.087,242,0,0,235,SILENT,p.Val162Val/c.486G>C,.,NA,NA,NA
MMEL1,,NON_SYNONYMOUS_CODING,MODERATE,1:2535624,T,A,p.Met296Leu,c.886T>A,21,0.131,160,0,0,150,MISSENSE,p.Met296Leu/c.886T>A:p.Met305Leu/c.913T>A,.,NA,NA,NA
NCAPH,,NON_SYNONYMOUS_CODING,MODERATE,2:97033103,G,C,p.Asp104His,c.310G>C,16,0.113,142,0,0,113,MISSENSE,p.Asp104His/c.310G>C:p.Asp528His/c.1582G>C:p.Asp653His/c.1957G>C:p.Asp664His/c.1990G>C,.,NA,NA,NA
NDNL2,,SYNONYMOUS_CODING,LOW,15:29561448,G,A,p.Leu154Leu,c.462G>A,41,0.143,287,0,0,211,SILENT,p.Leu154Leu/c.462G>A,.,NA,NA,NA
NYX,,SYNONYMOUS_CODING,LOW,X:41333762,G,A,p.Glu352Glu,c.1056G>A,15,0.089,168,0,0,151,SILENT,p.Glu352Glu/c.1056G>A,.,NA,NA,NA
OSBPL5,,NON_SYNONYMOUS_CODING,MODERATE,11:3140780,C,G,p.Asp141His,c.421C>G,19,0.107,178,1,0.005,186,MISSENSE,p.Asp141His/c.421C>G:p.Asp162His/c.484C>G:p.Asp230His/c.688C>G,.,NA,NA,NA
OTUD6B,,SYNONYMOUS_CODING,LOW,8:92086121,A,G,p.Ser129Ser,c.387A>G,15,0.143,105,0,0,126,SILENT,p.Ser129Ser/c.387A>G,.,NA,NA,NA
PALD1,,SYNONYMOUS_CODING,LOW,10:72297632,G,C,p.Leu431Leu,c.1293G>C,17,0.097,175,0,0,177,SILENT,p.Leu431Leu/c.1293G>C,.,364269,364269,NA
PARVA,,NON_SYNONYMOUS_CODING,MODERATE,11:12535076,T,C,p.Trp270Arg,c.808T>C,25,0.117,213,0,0,229,MISSENSE,p.Trp270Arg/c.808T>C,.,NA,NA,NA
PCDH20,,NON_SYNONYMOUS_CODING,MODERATE,13:61986127,C,A,p.Arg702Ile,c.2105C>A,18,0.164,110,0,0,138,MISSENSE,p.Arg702Ile/c.2105C>A,.,NA,NA,NA
PCF11,,STOP_GAINED,HIGH,11:82878679,C,T,p.Gln742*,c.2224C>T,22,0.151,146,0,0,193,NONSENSE,p.Gln742*/c.2224C>T,.,NA,NA,NA
PHIP,,SYNONYMOUS_CODING,LOW,6:79711725,C,T,p.Leu590Leu,c.1770C>T,12,0.113,106,1,0.006,162,SILENT,p.Leu590Leu/c.1770C>T,.,NA,NA,NA
PIAS2,,NON_SYNONYMOUS_CODING,MODERATE,18:44409770,A,T,p.Asp131Glu,c.393A>T,21,0.105,200,0,0,196,MISSENSE,p.Asp131Glu/c.393A>T:p.Asp412Glu/c.1236A>T:p.Asp421Glu/c.1263A>T,.,NA,NA,NA
POLR1C,,SYNONYMOUS_CODING,LOW,6:43488683,C,G,p.Ala223Ala,c.669C>G,14,0.136,103,0,0,125,SILENT,p.Ala223Ala/c.669C>G:p.Ala273Ala/c.819C>G,.,NA,NA,NA
POMGNT1,,NON_SYNONYMOUS_CODING,MODERATE,1:46662711,T,C,p.Lys34Glu,c.100T>C,24,0.163,147,0,0,148,MISSENSE,p.Lys34Glu/c.100T>C:p.Lys56Glu/c.166T>C,.,NA,NA,NA
PRDM13,,SYNONYMOUS_CODING,LOW,6:100054958,C,T,p.Cys16Cys,c.48C>T,17,0.106,160,0,0,115,SILENT,p.Cys16Cys/c.48C>T,.,NA,NA,NA
PTCHD1,,STOP_GAINED,HIGH,X:23411034,G,T,p.Glu467*,c.1399G>T,18,0.159,113,0,0,136,NONSENSE,p.Glu467*/c.1399G>T,.,NA,NA,NA
RBMX2,,SYNONYMOUS_CODING,LOW,X:129545432,T,G,p.Ala138Ala,c.414T>G,20,0.194,103,0,0,118,SILENT,p.Ala138Ala/c.414T>G,.,NA,NA,NA
RREB1,,NON_SYNONYMOUS_CODING,MODERATE,6:7182275,C,T,p.Ser44Leu,c.131C>T,11,0.111,99,0,0,130,MISSENSE,p.Ser44Leu/c.131C>T,.,NA,NA,NA
RUVBL2,,NON_SYNONYMOUS_CODING,MODERATE,19:49518405,A,G,p.Lys372Glu,c.1114A>G,11,0.102,108,0,0,109,MISSENSE,p.Lys372Glu/c.1114A>G:p.Lys417Glu/c.1249A>G,.,NA,NA,NA
SEMA5A,,NON_SYNONYMOUS_CODING,MODERATE,5:9122828,G,A,p.Ala574Val,c.1721G>A,14,0.093,150,0,0,113,MISSENSE,p.Ala574Val/c.1721G>A,.,NA,NA,NA
SETD1B,,NON_SYNONYMOUS_CODING,MODERATE,12:122252663,G,A,p.Gly848Ser,c.2542G>A,31,0.129,240,0,0,260,MISSENSE,p.Gly848Ser/c.2542G>A,.,NA,NA,NA
SF3B1,Y,NON_SYNONYMOUS_CODING,MODERATE,2:198266776,T,A,p.Tyr719Phe,c.2156T>A,12,0.145,83,0,0,116,MISSENSE,p.Tyr719Phe/c.2156T>A,.,NA,NA,Y
SIX5,,NON_SYNONYMOUS_CODING,MODERATE,19:46271982,C,T,p.Ala41Thr,c.121C>T,10,0.156,64,0,0,8,MISSENSE,p.Ala41Thr/c.121C>T:p.Gly44Asp/c.131C>T,.,NA,NA,NA
SLC6A7,,NON_SYNONYMOUS_CODING,MODERATE,5:149576628,A,T,p.Ile125Phe,c.373A>T,37,0.184,201,0,0,213,MISSENSE,p.Ile125Phe/c.373A>T,.,NA,NA,NA
SMARCA2,,SYNONYMOUS_CODING,LOW,9:2054642,G,T,p.Leu364Leu,c.1092G>T,15,0.074,202,1,0.004,231,SILENT,p.Leu364Leu/c.1092G>T,.,NA,NA,NA
SMOX,,NON_SYNONYMOUS_CODING,MODERATE,20:4162490,C,T,p.Pro159Leu,c.476C>T,21,0.12,175,0,0,173,MISSENSE,p.Pro159Leu/c.476C>T:p.Pro16Leu/c.47C>T,.,NA,NA,NA
SNURF,,NON_SYNONYMOUS_CODING,MODERATE,15:25207304,G,A,p.Glu20Lys,c.58G>A,17,0.105,162,0,0,200,MISSENSE,p.Glu20Lys/c.58G>A,.,959949,959949,NA
SORBS3,,NON_SYNONYMOUS_CODING,MODERATE,8:22432367,C,G,p.Thr142Ser,c.425C>G,13,0.099,131,0,0,139,MISSENSE,p.Thr142Ser/c.425C>G,.,NA,NA,NA
SPEG,,NON_SYNONYMOUS_CODING,MODERATE,2:220349098,G,A,p.Glu2305Lys,c.6913G>A,32,0.114,281,0,0,198,MISSENSE,p.Glu2305Lys/c.6913G>A,.,NA,NA,NA
SRP72,,NON_SYNONYMOUS_CODING,MODERATE,4:57356569,A,C,p.Lys225Thr,c.674A>C,11,0.136,81,0,0,91,MISSENSE,p.Lys225Thr/c.674A>C:p.Lys403Thr/c.1208A>C:p.Lys464Thr/c.1391A>C,.,NA,NA,NA
SYNPO2L,,STOP_GAINED,HIGH,10:75415646,G,C,p.Ser12*,c.35G>C,18,0.101,178,0,0,165,NONSENSE,p.Ser12*/c.35G>C,.,NA,NA,NA
TFE3,,NON_SYNONYMOUS_CODING,MODERATE,X:48896697,C,T,p.Val157Ile,c.469C>T,15,0.076,198,0,0,236,MISSENSE,p.Val157Ile/c.469C>T,rs149950072,NA,NA,Y
TP53INP1,,NON_SYNONYMOUS_CODING,MODERATE,8:95952320,C,G,p.Asp81His,c.241C>G,14,0.159,88,0,0,75,MISSENSE,p.Asp81His/c.241C>G,.,NA,NA,NA
TRADD,,NON_SYNONYMOUS_CODING,MODERATE,16:67189155,C,T,p.Ala158Thr,c.472C>T,28,0.072,391,0,0,255,MISSENSE,p.Ala158Thr/c.472C>T:p.Ala98Thr/c.292C>T,.,NA,NA,NA
TRIM37,,NON_SYNONYMOUS_CODING,MODERATE,17:57139940,T,A,p.Leu184Phe,c.552T>A,17,0.179,95,0,0,120,MISSENSE,p.Leu184Phe/c.552T>A:p.Leu188Phe/c.564T>A:p.Leu276Phe/c.828T>A:p.Leu310Phe/c.930T>A,.,NA,NA,NA
TRIM55,,NON_SYNONYMOUS_CODING,MODERATE,8:67066415,C,T,p.Pro457Leu,c.1370C>T,27,0.148,182,1,0.006,181,MISSENSE,p.Pro457Leu/c.1370C>T,.,NA,NA,NA
TRIQK,,NON_SYNONYMOUS_CODING,MODERATE,8:93929192,A,C,p.Ile9Arg,c.26A>C,12,0.203,59,0,0,58,MISSENSE,p.Ile9Arg/c.26A>C,.,NA,NA,NA
TRPC5,,NON_SYNONYMOUS_CODING,MODERATE,X:111195602,T,A,p.Asp16Val,c.47T>A,19,0.142,134,0,0,146,MISSENSE,p.Asp16Val/c.47T>A,.,NA,NA,NA
TTN,,NON_SYNONYMOUS_CODING,MODERATE,2:179614823,G,T,p.Pro4102Thr,c.12304G>T,21,0.188,112,0,0,118,MISSENSE,p.Pro4102Thr/c.12304G>T,.,NA,NA,NA
TXNDC5,,SYNONYMOUS_CODING,LOW,6:7899881,C,T,p.Val149Val,c.447C>T,16,0.093,172,0,0,181,SILENT,p.Val149Val/c.447C>T:p.Val41Val/c.123C>T:p.Val77Val/c.231C>T,.,NA,NA,NA
VCPIP1,,SYNONYMOUS_CODING,LOW,8:67547210,A,T,p.Thr1065Thr,c.3195A>T,37,0.243,152,0,0,150,SILENT,p.Thr1065Thr/c.3195A>T,.,NA,NA,NA
VGLL4,,NON_SYNONYMOUS_CODING,MODERATE,3:11643371,C,A,p.Asp5Tyr,c.13C>A,19,0.145,131,0,0,169,MISSENSE,p.Asp5Tyr/c.13C>A:p.Asp60Tyr/c.178C>A:p.Asp64Tyr/c.190C>A:p.Asp69Tyr/c.205C>A:p.Asp70Tyr/c.208C>A,.,NA,NA,NA
WDR52,,SYNONYMOUS_CODING,LOW,3:113152437,C,T,p.Leu25Leu,c.75C>T,13,0.118,110,1,0.011,90,SILENT,p.Leu25Leu/c.75C>T,.,NA,NA,NA
WEE2,,SYNONYMOUS_CODING,LOW,7:141424051,C,T,p.Phe174Phe,c.522C>T,17,0.187,91,0,0,109,SILENT,p.Phe174Phe/c.522C>T:p.Phe399Phe/c.1197C>T,.,NA,NA,NA
ZNF217,Y,NON_SYNONYMOUS_CODING,MODERATE,20:52198923,C,T,p.Arg148Lys,c.443C>T,77,0.192,402,1,0.003,374,MISSENSE,p.Arg148Lys/c.443C>T,.,NA,NA,NA
ZNF280B,,NON_SYNONYMOUS_CODING,MODERATE,22:22842393,G,T,p.Ala444Glu,c.1331G>T,43,0.204,211,0,0,198,MISSENSE,p.Ala444Glu/c.1331G>T,.,NA,NA,NA
ZNF672,,NON_SYNONYMOUS_CODING,MODERATE,1:249141538,G,C,p.Ser22Thr,c.65G>C,39,0.134,290,0,0,323,MISSENSE,p.Ser22Thr/c.65G>C,.,NA,NA,NA
C8orf73,,FRAME_SHIFT,HIGH,8:144649541,G,GC,p.X676X,c.2027*>+C,20,0.645,31,0,0,2,FRAME_SHIFT,p.X676X/c.2027*>+C:p.X7X/c.20*>+C,.,NA,NA,NA
CA4,,FRAME_SHIFT,HIGH,17:58236606,CAG,C,p.X126X,c.377*>-AG,35,0.104,335,0,0,361,FRAME_SHIFT,p.X126X/c.377*>-AG:p.X254X/c.761*>-AG,.,NA,NA,NA
CENPF,,FRAME_SHIFT,HIGH,1:214792014,TAACAC,T,p.X153X,c.459*>-AACAC,10,0.119,84,0,0,81,FRAME_SHIFT,p.X153X/c.459*>-AACAC,.,NA,NA,NA
DSP,,FRAME_SHIFT,HIGH,6:7585261,CAGTA,C,p.X1990X,c.5970*>-AGTA,31,0.149,208,0,0,205,FRAME_SHIFT,p.X1990X/c.5970*>-AGTA:p.X2589X/c.7767*>-AGTA,.,NA,NA,NA
RC3H2,,FRAME_SHIFT,HIGH,9:125642147,CAG,C,p.X237X,c.710*>-AG,16,0.12,133,0,0,147,FRAME_SHIFT,p.X237X/c.710*>-AG:p.X366X/c.1097*>-AG,.,NA,NA,NA
SNX6,,FRAME_SHIFT,HIGH,14:35073372,GT,G,p.X8X,c.24*>-T,45,0.18,250,1,0.003,295,FRAME_SHIFT,p.X8X/c.24*>-T,.,NA,NA,NA