Supplementary table S5.1,,,,,,,,,,,,,,,,,,,,
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
AIM2,,NON_SYNONYMOUS_CODING,MODERATE,1:159033289,T,G,p.His331Pro,c.992T>G,17,0.066,258,0,0,201,MISSENSE,p.His331Pro/c.992T>G,rs202163702,NA,NA,NA
ALPK2,,SYNONYMOUS_CODING,LOW,18:56246565,A,G,p.Ser481Ser,c.1443A>G,13,0.07,185,0,0,150,SILENT,p.Ser481Ser/c.1443A>G,.,NA,NA,NA
C11orf71,,NON_SYNONYMOUS_CODING,MODERATE,11:114270788,A,G,p.Phe89Ser,c.266A>G,15,0.041,370,0,0,196,MISSENSE,p.Phe89Ser/c.266A>G,.,NA,NA,NA
CSMD3,,NON_SYNONYMOUS_CODING,MODERATE,8:113650978,C,T,p.Arg1054His,c.3161C>T,12,0.051,236,0,0,248,MISSENSE,p.Arg1054His/c.3161C>T:p.Arg1118His/c.3353C>T:p.Arg1158His/c.3473C>T:p.Arg498His/c.1493C>T,.,x2 ids,1095136:1154930,NA
FLII,,SYNONYMOUS_CODING,LOW,17:18151157,C,T,p.Gln681Gln,c.2043C>T,15,0.049,305,0,0,113,SILENT,p.Gln681Gln/c.2043C>T:p.Gln712Gln/c.2136C>T:p.Gln756Gln/c.2268C>T:p.Gln767Gln/c.2301C>T,.,NA,NA,NA
GALNT12,,NON_SYNONYMOUS_CODING,MODERATE,9:101594160,G,A,p.Asp280Asn,c.838G>A,36,0.15,240,0,0,194,MISSENSE,p.Asp280Asn/c.838G>A,.,NA,NA,NA
GUK1,,NON_SYNONYMOUS_CODING,MODERATE,1:228333288,C,T,p.Pro98Ser,c.292C>T,26,0.07,372,0,0,141,MISSENSE,p.Pro98Ser/c.292C>T,.,NA,NA,NA
HACE1,,NON_SYNONYMOUS_CODING,MODERATE,6:105281023,C,T,p.Arg109Gln,c.326C>T,100,0.2,501,0,0,255,MISSENSE,p.Arg109Gln/c.326C>T:p.Arg143Gln/c.428C>T,.,3393739,3393739,NA
HTT,,NON_SYNONYMOUS_CODING,MODERATE,4:3201509,G,A,p.Gly1807Ser,c.5419G>A,21,0.128,164,0,0,113,MISSENSE,p.Gly1807Ser/c.5419G>A,.,NA,NA,NA
IKZF1,,SYNONYMOUS_CODING,LOW,7:50468106,C,T,p.Asp217Asp,c.651C>T,32,0.073,440,0,0,185,SILENT,p.Asp217Asp/c.651C>T:p.Asp304Asp/c.912C>T:p.Asp360Asp/c.1080C>T:p.Asp405Asp/c.1215C>T:p.Asp447Asp/c.1341C>T,rs143013761,NA,NA,Y
MDN1,,NON_SYNONYMOUS_CODING,MODERATE,6:90388345,C,T,p.Asp4129Asn,c.12385C>T,10,0.028,362,0,0,244,MISSENSE,p.Asp4129Asn/c.12385C>T,.,NA,NA,NA
MTNR1B,,NON_SYNONYMOUS_CODING,MODERATE,11:92714994,C,T,p.Ala202Val,c.605C>T,34,0.083,412,0,0,123,MISSENSE,p.Ala202Val/c.605C>T,.,NA,NA,NA
MYH14,,SYNONYMOUS_CODING,LOW,19:50752987,G,A,p.Leu513Leu,c.1539G>A,48,0.235,204,0,0,92,SILENT,p.Leu513Leu/c.1539G>A:p.Leu521Leu/c.1563G>A,.,NA,NA,NA
NLRP1,,NON_SYNONYMOUS_CODING,MODERATE,17:5418234,G,A,p.Thr1347Met,c.4040G>A,35,0.178,197,1,0.006,174,MISSENSE,p.Thr1347Met/c.4040G>A:p.Thr1377Met/c.4130G>A:p.Thr1391Met/c.4172G>A:p.Thr1421Met/c.4262G>A,.,NA,NA,NA
PCLO,,NON_SYNONYMOUS_CODING,MODERATE,7:82581299,C,T,p.Met2990Ile,c.8970C>T,34,0.26,131,0,0,157,MISSENSE,p.Met2990Ile/c.8970C>T,.,NA,NA,NA
PCTP,,SYNONYMOUS_CODING,LOW,17:53848489,C,T,p.Asn22Asn,c.66C>T,10,0.074,135,0,0,103,SILENT,p.Asn22Asn/c.66C>T:p.Asn94Asn/c.282C>T,.,NA,NA,NA
PIK3CA,Y,NON_SYNONYMOUS_CODING,MODERATE,3:178952085,A,G,p.His1047Arg,c.3140A>G,102,0.376,271,0,0,311,MISSENSE,p.His1047Arg/c.3140A>G,rs121913279,x5 ids,775:776:94986:94987:249874,Y
PLA2G7,,NON_SYNONYMOUS_CODING,MODERATE,6:46672959,C,A,p.Asp374Tyr,c.1120C>A,14,0.246,57,0,0,78,MISSENSE,p.Asp374Tyr/c.1120C>A,.,NA,NA,NA
PRR14L,,SYNONYMOUS_CODING,LOW,22:32113141,G,A,p.Cys228Cys,c.684G>A,32,0.254,126,0,0,294,SILENT,p.Cys228Cys/c.684G>A,rs375439944,NA,NA,NA
SMC1A,,NON_SYNONYMOUS_CODING,MODERATE,X:53432289,G,A,p.Ser415Leu,c.1244G>A,12,0.081,148,0,0,160,MISSENSE,p.Ser415Leu/c.1244G>A:p.Ser649Leu/c.1946G>A,.,NA,NA,NA
STIP1,,SYNONYMOUS_CODING,LOW,11:63970365,C,T,p.Ile20Ile,c.60C>T,16,0.15,107,0,0,103,SILENT,p.Ile20Ile/c.60C>T:p.Ile397Ile/c.1191C>T:p.Ile421Ile/c.1263C>T:p.Ile468Ile/c.1404C>T,.,NA,NA,NA
SYNM,,NON_SYNONYMOUS_CODING,MODERATE,15:99671927,G,T,p.Ser1120Ile,c.3359G>T,15,0.079,189,0,0,156,MISSENSE,p.Ser1120Ile/c.3359G>T:p.Ser835Ile/c.2504G>T,.,NA,NA,NA
THEG,,NON_SYNONYMOUS_CODING,MODERATE,19:375778,G,A,p.Pro65Ser,c.193G>A,68,0.234,290,0,0,192,MISSENSE,p.Pro65Ser/c.193G>A,.,NA,NA,NA
TP53,Y,START_LOST,HIGH,17:7578532,A,T,p.Met1?,c.2A>T,39,0.336,116,0,0,85,MISSENSE,p.Met1?/c.2A>T,rs28934873,x20 ids,11781:43723:43730:45979:132890:437605:437606:437607:437608:1559495:1559496:1559497:1559498:1640867:1640868:1640869:1640870:1640871:3388221:3388222,Y
TTC7B,,NON_SYNONYMOUS_CODING,MODERATE,14:91282617,G,A,p.Ser8Leu,c.23G>A,22,0.162,136,0,0,68,MISSENSE,p.Ser8Leu/c.23G>A,.,NA,NA,NA
VSTM2A,,SYNONYMOUS_CODING,LOW,7:54636706,G,A,p.Ala213Ala,c.639G>A,19,0.345,55,0,0,68,SILENT,p.Ala213Ala/c.639G>A,.,NA,NA,NA
ZNF407,,NON_SYNONYMOUS_CODING,MODERATE,18:72346623,C,A,p.Asn1216Lys,c.3648C>A,18,0.079,229,0,0,197,MISSENSE,p.Asn1216Lys/c.3648C>A,.,NA,NA,NA
MBD6,,FRAME_SHIFT,HIGH,12:57919188,GCCCT,G,p.X146X,c.438*>-CCCT,63,0.281,224,0,0,159,FRAME_SHIFT,p.X146X/c.438*>-CCCT:p.X50X/c.150*>-CCCT,.,1734935,1734935,NA
PMS2,Y,FRAME_SHIFT,HIGH,7:6037053,A,ATAATCTTTTTTAGTAAGTAG,p.X130X,c.388*>+TAATCTTTTTTAGTAAGTAG,13,0.143,91,0,0,68,FRAME_SHIFT,p.X130X/c.388*>+TAATCTTTTTTAGTAAGTAG:p.X189X/c.565*>+TAATCTTTTTTAGTAAGTAG:p.X236X/c.706*>+TAATCTTTTTTAGTAAGTAG,.,NA,NA,Y
RUNX1,Y,FRAME_SHIFT,HIGH,21:36252976,A,AG,p.X102X,c.304*>+G,26,0.268,97,0,0,102,FRAME_SHIFT,p.X102X/c.304*>+G:p.X105X/c.313*>+G:p.X116X/c.346*>+G:p.X117X/c.349*>+G:p.X129X/c.385*>+G,.,96549,96549,Y