Supplementary table S4.5,,,,,,,,,,,,,,,,,,,,
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
ACTN1,,STOP_GAINED,HIGH,14:69369262,G,A,p.Arg167*,c.499G>A,32,0.32,100,0,0,192,NONSENSE,p.Arg167*/c.499G>A:p.Arg211*/c.631G>A:p.Arg232*/c.694G>A,rs368332884,NA,NA,NA
AQP2,,NON_SYNONYMOUS_CODING,MODERATE,12:50349221,T,C,p.Ser216Pro,c.646T>C,15,0.132,114,0,0,71,MISSENSE,p.Ser216Pro/c.646T>C,rs104894329,NA,NA,NA
ARFGAP2,,SYNONYMOUS_CODING,LOW,11:47198381,G,C,p.Thr8Thr,c.24G>C,30,0.221,136,0,0,228,SILENT,p.Thr8Thr/c.24G>C,.,NA,NA,NA
ASCC3,,NON_SYNONYMOUS_CODING,MODERATE,6:101247387,C,T,p.Val397Ile,c.1189C>T,63,0.139,452,0,0,424,MISSENSE,p.Val397Ile/c.1189C>T,rs376345263,NA,NA,NA
CACNA1B,,SYNONYMOUS_CODING,LOW,9:140946601,G,A,p.Leu1256Leu,c.3768G>A,17,0.23,74,0,0,60,SILENT,p.Leu1256Leu/c.3768G>A:p.Leu1257Leu/c.3771G>A:p.Leu452Leu/c.1356G>A,.,1461463,1461463,NA
CCDC166,,NON_SYNONYMOUS_CODING,MODERATE,8:144789714,C,G,p.Arg138Pro,c.413C>G,39,0.218,179,0,0,15,MISSENSE,p.Arg138Pro/c.413C>G:p.Arg157Pro/c.470C>G,.,NA,NA,NA
CEP350,,NON_SYNONYMOUS_CODING,MODERATE,1:179965695,C,T,p.His109Tyr,c.325C>T,28,0.171,164,1,0.006,175,MISSENSE,p.His109Tyr/c.325C>T:p.His135Tyr/c.403C>T,.,NA,NA,NA
CKAP5,,NON_SYNONYMOUS_CODING,MODERATE,11:46786718,C,T,p.Gly1167Glu,c.3500C>T,40,0.244,164,0,0,246,MISSENSE,p.Gly1167Glu/c.3500C>T,.,NA,NA,NA
CNKSR1,,NON_SYNONYMOUS_CODING,MODERATE,1:26510721,G,A,p.Val315Ile,c.943G>A,52,0.248,210,0,0,112,MISSENSE,p.Val315Ile/c.943G>A:p.Val322Ile/c.964G>A:p.Val57Ile/c.169G>A,rs199807460,NA,NA,NA
CORO1A,,STOP_GAINED,HIGH,16:30199273,C,G,p.Ser291*,c.872C>G,90,0.218,413,0,0,329,NONSENSE,p.Ser291*/c.872C>G,.,NA,NA,NA
DOCK2,,SYNONYMOUS_CODING,LOW,5:169145679,G,A,p.Leu209Leu,c.627G>A,52,0.413,126,0,0,214,SILENT,p.Leu209Leu/c.627G>A:p.Leu717Leu/c.2151G>A,.,NA,NA,NA
DRD3,,NON_SYNONYMOUS_CODING,MODERATE,3:113890776,C,T,p.Gly22Ser,c.64C>T,28,0.192,146,0,0,66,MISSENSE,p.Gly22Ser/c.64C>T,.,NA,NA,NA
DRP2,,NON_SYNONYMOUS_CODING,MODERATE,X:100515548,C,T,p.Arg860Cys,c.2578C>T,17,0.354,48,0,0,62,MISSENSE,p.Arg860Cys/c.2578C>T:p.Arg938Cys/c.2812C>T,rs141816203,NA,NA,NA
DYRK2,,NON_SYNONYMOUS_CODING,MODERATE,12:68051318,G,A,p.Val138Met,c.412G>A,47,0.29,162,0,0,188,MISSENSE,p.Val138Met/c.412G>A:p.Val211Met/c.631G>A,.,NA,NA,NA
GANAB,,NON_SYNONYMOUS_CODING,MODERATE,11:62401813,T,C,p.Ile199Val,c.595T>C,20,0.217,92,0,0,158,MISSENSE,p.Ile199Val/c.595T>C:p.Ile85Val/c.253T>C,.,NA,NA,NA
GRIK2,,NON_SYNONYMOUS_CODING,MODERATE,6:102124540,A,T,p.Tyr146Phe,c.437A>T,17,0.279,61,0,0,65,MISSENSE,p.Tyr146Phe/c.437A>T:p.Tyr195Phe/c.584A>T,.,NA,NA,NA
HINT1,,NON_SYNONYMOUS_CODING,MODERATE,5:130495253,G,C,p.Leu90Val,c.268G>C,18,0.462,39,0,0,68,MISSENSE,p.Leu90Val/c.268G>C,.,NA,NA,NA
IL1RL1,,NON_SYNONYMOUS_CODING,MODERATE,2:102968116,C,A,p.Ala469Asp,c.1406C>A,64,0.261,245,0,0,271,MISSENSE,p.Ala469Asp/c.1406C>A,.,NA,NA,NA
IMPG2,,SYNONYMOUS_CODING,LOW,3:100962658,C,T,p.Ser839Ser,c.2517C>T,26,0.195,133,0,0,171,SILENT,p.Ser839Ser/c.2517C>T,.,1254814,1254814,NA
KCMF1,,SYNONYMOUS_CODING,LOW,2:85255127,A,T,p.Thr44Thr,c.132A>T,16,0.216,74,0,0,114,SILENT,p.Thr44Thr/c.132A>T,.,NA,NA,NA
LCNL1,,NON_SYNONYMOUS_CODING,MODERATE,9:139878076,A,G,p.Asp13Gly,c.38A>G,32,0.376,85,1,0.01,98,MISSENSE,p.Asp13Gly/c.38A>G,.,NA,NA,NA
LENG9,,SYNONYMOUS_CODING,LOW,19:54974338,G,T,p.Arg146Arg,c.438G>T,31,0.15,207,0,0,139,SILENT,p.Arg146Arg/c.438G>T,.,NA,NA,NA
LENG9,,NON_SYNONYMOUS_CODING,MODERATE,19:54974339,C,T,p.Arg146His,c.437C>T,31,0.153,203,0,0,138,MISSENSE,p.Arg146His/c.437C>T,.,NA,NA,NA
LRRC36,,NON_SYNONYMOUS_CODING,MODERATE,16:67418869,T,A,p.His186Gln,c.558T>A,15,0.294,51,0,0,67,MISSENSE,p.His186Gln/c.558T>A:p.His489Gln/c.1467T>A:p.His593Gln/c.1779T>A:p.His714Gln/c.2142T>A,.,NA,NA,NA
LRRK1,,NON_SYNONYMOUS_CODING,MODERATE,15:101605617,C,T,p.Arg1656Trp,c.4966C>T,56,0.293,191,1,0.007,145,MISSENSE,p.Arg1656Trp/c.4966C>T:p.Arg1659Trp/c.4975C>T,.,NA,NA,NA
MRPL19,,NON_SYNONYMOUS_CODING,MODERATE,2:75882243,T,G,p.Asn237Lys,c.711T>G,10,0.233,43,0,0,107,MISSENSE,p.Asn237Lys/c.711T>G:p.Asn24Lys/c.72T>G,.,NA,NA,NA
MSH2,Y,NON_SYNONYMOUS_CODING,MODERATE,2:47637368,T,A,p.Ser102Thr,c.304T>A,19,0.317,60,0,0,129,MISSENSE,p.Ser102Thr/c.304T>A:p.Ser168Thr/c.502T>A,.,1408245,1408245,Y
MYO10,,SYNONYMOUS_CODING,LOW,5:16764380,G,T,p.Ile435Ile,c.1305G>T,34,0.129,264,0,0,276,SILENT,p.Ile435Ile/c.1305G>T:p.Ile446Ile/c.1338G>T,.,NA,NA,NA
NAV3,,NON_SYNONYMOUS_CODING,MODERATE,12:78592902,A,T,p.Ser16Cys,c.46A>T,35,0.327,107,0,0,166,MISSENSE,p.Ser16Cys/c.46A>T,.,NA,NA,NA
NEFM,,NON_SYNONYMOUS_CODING,MODERATE,8:24776087,G,A,p.Ala531Thr,c.1591G>A,13,0.52,25,0,0,34,MISSENSE,p.Ala531Thr/c.1591G>A:p.Ala689Thr/c.2065G>A:p.Ala868Thr/c.2602G>A:p.Ala907Thr/c.2719G>A,.,NA,NA,NA
NOD1,,NON_SYNONYMOUS_CODING,MODERATE,7:30491732,T,C,p.Asn434Ser,c.1301T>C,92,0.322,286,0,0,149,MISSENSE,p.Asn434Ser/c.1301T>C,.,NA,NA,NA
OR4C15,,STOP_GAINED,HIGH,11:55321918,G,T,p.Gly46*,c.136G>T,46,0.274,168,0,0,185,NONSENSE,p.Gly46*/c.136G>T,.,NA,NA,NA
PHLPP1,,SYNONYMOUS_CODING,LOW,18:60563062,T,C,p.Ala242Ala,c.726T>C,32,0.405,79,0,0,202,SILENT,p.Ala242Ala/c.726T>C:p.Ala754Ala/c.2262T>C,.,NA,NA,NA
PKHD1L1,,STOP_GAINED,HIGH,8:110477137,T,G,p.Tyr2692*,c.8076T>G,39,0.217,180,0,0,199,NONSENSE,p.Tyr2692*/c.8076T>G,.,NA,NA,NA
PLEC,,NON_SYNONYMOUS_CODING,MODERATE,8:144997504,G,C,p.Thr2166Ser,c.6497G>C,58,0.198,293,0,0,74,MISSENSE,p.Thr2166Ser/c.6497G>C:p.Thr2176Ser/c.6527G>C:p.Thr2184Ser/c.6551G>C:p.Thr2198Ser/c.6593G>C:p.Thr2202Ser/c.6605G>C:p.Thr2221Ser/c.6662G>C:p.Thr2225Ser/c.6674G>C:p.Thr2335Ser/c.7004G>C,.,NA,NA,NA
PODN,,NON_SYNONYMOUS_CODING,MODERATE,1:53540293,C,T,p.Ala170Val,c.509C>T,70,0.173,404,1,0.004,282,MISSENSE,p.Ala170Val/c.509C>T:p.Ala189Val/c.566C>T,rs140637273,NA,NA,NA
PPP1R15B,,STOP_LOST,HIGH,1:204375222,A,C,p.*714Glyext*?,c.2140A>C,14,0.116,121,0,0,249,MISSENSE,p.*714Glyext*?/c.2140A>C,.,NA,NA,NA
PSKH2,,NON_SYNONYMOUS_CODING,MODERATE,8:87081724,G,A,p.Ala43Val,c.128G>A,265,0.502,528,1,0.009,115,MISSENSE,p.Ala43Val/c.128G>A,.,NA,NA,NA
PWP1,,NON_SYNONYMOUS_CODING,MODERATE,12:108102739,G,A,p.Ala310Thr,c.928G>A,11,0.355,31,0,0,69,MISSENSE,p.Ala310Thr/c.928G>A:p.Ala372Thr/c.1114G>A,.,NA,NA,NA
RANBP3,,NON_SYNONYMOUS_CODING,MODERATE,19:5923835,T,A,p.Thr235Ser,c.703T>A,38,0.494,77,0,0,97,MISSENSE,p.Thr235Ser/c.703T>A:p.Thr290Ser/c.868T>A:p.Thr295Ser/c.883T>A:p.Thr358Ser/c.1072T>A:p.Thr363Ser/c.1087T>A:p.Thr82Ser/c.244T>A,rs528535352,NA,NA,NA
RSPO4,,SYNONYMOUS_CODING,LOW,20:944738,G,A,p.Gly145Gly,c.435G>A,15,0.181,83,0,0,63,SILENT,p.Gly145Gly/c.435G>A,rs201319898,1029374,1029374,NA
SRP72,,NON_SYNONYMOUS_CODING,MODERATE,4:57333821,G,C,p.Gly7Ala,c.20G>C,43,0.312,138,0,0,156,MISSENSE,p.Gly7Ala/c.20G>C,rs139502866,NA,NA,NA
STIL,,NON_SYNONYMOUS_CODING,MODERATE,1:47745938,C,G,p.Arg684Thr,c.2051C>G,15,0.185,81,0,0,48,MISSENSE,p.Arg684Thr/c.2051C>G:p.Arg70Thr/c.209C>G:p.Arg731Thr/c.2192C>G,.,NA,NA,NA
SYCP3,,SYNONYMOUS_CODING,LOW,12:102125435,G,T,p.Arg155Arg,c.463G>T,10,0.263,38,0,0,90,SILENT,p.Arg155Arg/c.463G>T,.,1677288,1677288,NA
SYT5,,SYNONYMOUS_CODING,LOW,19:55689588,C,A,p.Gly76Gly,c.228C>A,35,0.357,98,0,0,85,SILENT,p.Gly76Gly/c.228C>A,.,NA,NA,NA
TP53,Y,NON_SYNONYMOUS_CODING,MODERATE,17:7578406,C,T,p.Arg175His,c.524C>T,73,0.44,166,1,0.01,100,MISSENSE,p.Arg175His/c.524C>T:p.Arg43His/c.128C>T:p.Arg82His/c.245C>T,rs28934578,x14 ids,10648:10718:45416:99022:99023:99024:99914:1640851:1679508:1679509:1679510:1679511:1679512:3355994,Y
USP35,,NON_SYNONYMOUS_CODING,MODERATE,11:77921332,T,G,p.Phe379Val,c.1135T>G,12,0.027,440,0,0,216,MISSENSE,p.Phe379Val/c.1135T>G:p.Phe397Val/c.1189T>G:p.Phe542Val/c.1624T>G:p.Phe811Val/c.2431T>G,.,NA,NA,NA
WNT3A,,NON_SYNONYMOUS_CODING,MODERATE,1:228246837,G,A,p.Glu244Lys,c.730G>A,162,0.235,689,0,0,213,MISSENSE,p.Glu244Lys/c.730G>A,.,NA,NA,NA
ZBTB45,,SYNONYMOUS_CODING,LOW,19:59028654,G,A,p.Gly129Gly,c.387G>A,109,0.321,340,0,0,139,SILENT,p.Gly129Gly/c.387G>A,.,NA,NA,NA
ZIC3,,SYNONYMOUS_CODING,LOW,X:136649705,G,A,p.Glu285Glu,c.855G>A,11,0.033,333,1,0.006,181,SILENT,p.Glu285Glu/c.855G>A,.,NA,NA,NA
ZNF205,,SYNONYMOUS_CODING,LOW,16:3169354,C,T,p.Gly119Gly,c.357C>T,34,0.291,117,0,0,58,SILENT,p.Gly119Gly/c.357C>T:p.Gly231Gly/c.693C>T,rs558086377,NA,NA,NA
ZNF282,,SYNONYMOUS_CODING,LOW,7:148895445,C,T,p.Asp62Asp,c.186C>T,51,0.157,324,0,0,262,SILENT,p.Asp62Asp/c.186C>T,rs138579798,NA,NA,NA
ZNF790,,NON_SYNONYMOUS_CODING,MODERATE,19:37310961,C,A,p.Glu95Asp,c.285C>A,14,0.222,63,0,0,179,MISSENSE,p.Glu95Asp/c.285C>A,.,NA,NA,NA
ZNF839,,SYNONYMOUS_CODING,LOW,14:102805158,T,A,p.Ala103Ala,c.309T>A,26,0.22,118,0,0,185,SILENT,p.Ala103Ala/c.309T>A:p.Ala134Ala/c.402T>A:p.Ala152Ala/c.456T>A:p.Ala439Ala/c.1317T>A:p.Ala52Ala/c.156T>A:p.Ala54Ala/c.162T>A:p.Ala555Ala/c.1665T>A:p.Ala77Ala/c.231T>A,.,NA,NA,NA
SDHA,,FRAME_SHIFT,HIGH,5:236603,GC,G,p.X393X,c.1178*>-C,46,0.195,236,0,0,109,FRAME_SHIFT,p.X393X/c.1178*>-C:p.X441X/c.1322*>-C,.,NA,NA,NA