Supplementary Table 3.Sanger sequence confirmed NGS variants missed when false positive rate adjusted to zero
Gene / Transcript / cDNA location / Classification / Heterozygous Read Ratio / Coverage / Qscore / Internal MAF / Genomic RegionATM / NM_000051 / c.170G>A / Mutation / 34% / 94 / 564 / 0.02% / AT rich region
ATM / NM_000051 / c.170G>A / Mutation / 39% / 31 / 175 / 0.02% / AT rich region
ATM / NM_000051 / c.172G>T / VUS / 33% / 69 / 403 / 0.00% / AT rich region
ATM / NM_000051 / c.202A>G / VUS / 43% / 35 / 267 / 0.01% / AT rich region
ATM / NM_000051 / c.227G>A / VUS / 53% / 45 / 505 / 0.00% / Mosaic variant
ATM / NM_000051 / c.241A>G / VUS / 38% / 71 / 540 / 0.00% / AT rich region
ATM / NM_000051 / c.334G>A / VUS / 43% / 14 / 168 / 0.03% / AT rich region
ATM / NM_000051 / c.334G>A / VUS / 29% / 87 / 476 / 0.03% / AT rich region
ATM / NM_000051 / c.334G>A / VUS / 30% / 61 / 281 / 0.03% / AT rich region
ATM / NM_000051 / c.334G>A / VUS / 39% / 75 / 571 / 0.03% / AT rich region
ATM / NM_000051 / c.610G>A / VUS / 30% / 60 / 313 / 0.01% / AT rich region
ATM / NM_000051 / c.610G>A / VUS / 17% / 162 / 441 / 0.01% / AT rich region
ATM / NM_000051 / c.646G>T / VUS / 40% / 50 / 417 / 0.00% / AT rich region
ATM / NM_000051 / c.1009C>T / VUS / 50% / 36 / 422 / 0.02% / AT rich region
ATM / NM_000051 / c.1073A>G / VUS / 40% / 30 / 206 / 0.03% / AT rich region
ATM / NM_000051 / c.1168G>A / VUS / 28% / 123 / 498 / 0.00%
ATM / NM_000051 / c.1631T>C / VUS / 25% / 53 / 393 / 0.01%
ATM / NM_000051 / c.2377-5T>C / VUS / 42% / 74 / 622 / 0.00% / AT rich region
ATM / NM_000051 / c.3112G>C / VUS / 25% / 40 / 136 / 0.00% / AT rich region
ATM / NM_000051 / c.3154-5C>T / VUS / 40% / 25 / 290 / 0.01% / AT rich region
ATM / NM_000051 / c.3265G>T / VUS / 37% / 76 / 593 / 0.00%
ATM / NM_000051 / c.3665T>C / VUS / 37% / 73 / 578 / 0.00% / AT rich region
ATM / NM_000051 / c.4306C>T / VUS / 31% / 64 / 415 / 0.01% / AT rich region
ATM / NM_000051 / c.4631A>G / VUS / 23% / 69 / 313 / 0.00% / AT rich region
ATM / NM_000051 / c.4703A>G / VUS / 25% / 142 / 551 / 0.01% / AT rich region
ATM / NM_000051 / c.4724G>A / VUS / 35% / 55 / 291 / 0.01% / AT rich region
ATM / NM_000051 / c.4768C>T / VUS / 45% / 74 / 625 / 0.01% / AT rich region
ATM / NM_000051 / c.5009C>T / VUS / 42% / 19 / 138 / 0.00% / AT rich region
ATM / NM_000051 / c.5228C>T / VLP / 31% / 29 / 200 / 0.00%
ATM / NM_000051 / c.5456C>T / VUS / 33% / 21 / 140 / 0.00% / AT rich region
ATM / NM_000051 / c.5773G>T / Mutation / 20% / 201 / 611 / 0.00% / Mosaic variant
ATM / NM_000051 / c.5882A>G / VUS / 35% / 71 / 633 / 0.01% / AT rich region
ATM / NM_000051 / c.6112C>T / VUS / 12% / 601 / 613 / 0.00% / Mosaic variant
ATM / NM_000051 / c.6420C>A / VUS / 46% / 52 / 409 / 0.00% / AT rich region
ATM / NM_000051 / c.6604T>G / VUS / 45% / 55 / 602 / 0.00%
ATM / NM_000051 / c.7516-4G>T / VUS / 43% / 54 / 432 / 0.00% / AT rich region
ATM / NM_000051 / c.7571C>T / VUS / 27% / 161 / 625 / 0.00%
ATM / NM_000051 / c.7618G>A / VUS / 32% / 81 / 371 / 0.02% / AT rich region
ATM / NM_000051 / c.7618G>A / VUS / 32% / 56 / 345 / 0.02% / AT rich region
ATM / NM_000051 / c.7919C>T / VUS / 25% / 55 / 258 / 0.03% / AT rich region
ATM / NM_000051 / c.8308T>G / VUS / 15% / 517 / 639 / 0.00%
ATM / NM_000051 / c.8617G>A / VUS / 43% / 46 / 454 / 0.00% / AT rich region
ATM / NM_000051 / c.9021A>C / VUS / 13% / 380 / 308 / 0.00% / Mosaic variant
BARD1 / NM_000465 / c.26_40DEL15 / VUS / 33% / 45 / 497 / 0.01% / GC rich region
BARD1 / NM_000465 / c.173G>A / VUS / 13% / 52 / 40 / 0.00% / AT rich region
BARD1 / NM_000465 / c.266C>T / VUS / 38% / 86 / 603 / 0.01% / AT rich region
BARD1 / NM_000465 / c.346C>T / VUS / 66% / 29 / 367 / 0.02% / AT rich region
BARD1 / NM_000465 / c.716T>A / VUS / 59% / 32 / 432 / 0.02%
BARD1 / NM_000465 / c.841C>T / VUS / 45% / 58 / 520 / 0.01%
BARD1 / NM_000465 / c.1685C>T / VUS / 27% / 78 / 351 / 0.00%
BRCA1 / NM_007294 / c.16C>T / VUS / 45% / 69 / 773 / 0.00% / AT rich region
BRCA1 / NM_007294 / c.60A>C / VUS / 47% / 171 / 1692 / 0.00%
BRCA1 / NM_007294 / c.68_69DELAG / Mutation / 41% / 34 / 488 / 0.08%
BRCA1 / NM_007294 / c.68_69DELAG / Mutation / 42% / 119 / 1848 / 0.08%
BRCA1 / NM_007294 / c.181T>G / Mutation / 38% / 77 / 578 / 0.02% / AT rich region
BRCA1 / NM_007294 / c.181T>G / Mutation / 41% / 214 / 1585 / 0.02% / AT rich region
BRCA1 / NM_007294 / c.211A>G / Mutation / 49% / 114 / 1190 / 0.00% / AT rich region
BRCA1 / NM_007294 / c.230C>T / VUS / 46% / 173 / 1669 / 0.00%
BRCA1 / NM_007294 / c.594-2A>C / VUS / 50% / 147 / 1725 / 0.02%
BRCA1 / NM_007294 / c.641A>G / VUS / 48% / 172 / 1805 / 0.02%
BRCA1 / NM_007294 / c.964G>C / VUS / 44% / 124 / 1175 / 0.00%
BRCA1 / NM_007294 / c.1337G>T / VUS / 10% / 427 / 157 / 0.00% / Mosaic variant
BRCA1 / NM_007294 / c.2235A>C / VUS / 39% / 101 / 1418 / 0.00%
BRCA1 / NM_007294 / c.2236G>T / VUS / 38% / 99 / 1418 / 0.00%
BRCA1 / NM_007294 / c.2475DELC / Mutation / 38% / 87 / 1013 / 0.01%
BRCA1 / NM_007294 / c.2934T>G / Mutation / 47% / 114 / 1198 / 0.00% / AT rich region
BRCA1 / NM_007294 / c.3048_3052DUPTGAGA / Mutation / 36% / 44 / 584 / 0.01%
BRCA1 / NM_007294 / c.3289DUPA / Mutation / 45% / 75 / 859 / 0.00%
BRCA1 / NM_007294 / c.3759_3760DELTA / Mutation / 40% / 81 / 1158 / 0.00%
BRCA1 / NM_007294 / c.4432G>T / Mutation / 27% / 146 / 835 / 0.00%
BRCA1 / NM_007294 / c.5123C>T / VUS / 44% / 140 / 1284 / 0.00%
BRCA1 / NM_007294 / c.5324T>G / Mutation / 45% / 179 / 1758 / 0.01%
CDH1 / NM_004360 / c.8C>G / VUS / 42% / 242 / 2076 / 0.01% / GC rich region
CDH1 / NM_004360 / c.358G>A / VUS / 20% / 561 / 1928 / 0.00%
CDH1 / NM_004360 / c.521DUPA / Mutation / 49% / 175 / 1978 / 0.00%
CDH1 / NM_004360 / c.671G>A / VUS / 51% / 78 / 908 / 0.01%
CDH1 / NM_004360 / c.1223C>T / VUS / 44% / 207 / 1926 / 0.01%
CHEK2 / NM_007194 / c.470T>C / Mutation / 50% / 38 / 409 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.470T>C / Mutation / 59% / 46 / 567 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.470T>C / Mutation / 50% / 48 / 521 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.470T>C / Mutation / 27% / 81 / 598 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.470T>C / Mutation / 35% / 86 / 558 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.470T>C / Mutation / 51% / 63 / 576 / 0.36% / Pseudogene
CHEK2 / NM_007194 / c.542G>A / VUS / 31% / 59 / 311 / 0.01% / Pseudogene
CHEK2 / NM_007194 / c.663C>G / VUS / 52% / 31 / 302 / 0.01% / Pseudogene
CHEK2 / NM_007194 / c.848C>A / VUS / 26% / 125 / 541 / 0.00% / Pseudogene
CHEK2 / NM_007194 / c.855C>G / VUS / 47% / 17 / 152 / 0.00% / Pseudogene
CHEK2 / NM_007194 / c.896T>G / VUS / 12% / 81 / 52 / 0.00% / Pseudogene
CHEK2 / NM_007194 / c.904G>A / VUS / 40% / 48 / 350 / 0.01% / Pseudogene
CHEK2 / NM_007194 / c.1100DELC / Mutation / 27% / 84 / 589 / 0.48% / Pseudogene
CHEK2 / NM_007194 / c.1312G>T / VUS / 48% / 48 / 509 / 0.06% / Pseudogene
CHEK2 / NM_007194 / c.1461+1G>A / VLP / 11% / 625 / 223 / 0.00% / Mosaic variant
MSH2 / NM_000251 / c.-254G>C / VUS / 49% / 210 / 2278 / 0.01%
MSH2 / NM_000251 / c.1A>C / VUS / 46% / 114 / 1137 / 0.01%
MSH2 / NM_000251 / c.79C>A / VUS / 50% / 96 / 1111 / 0.00% / GC rich region
MSH2 / NM_000251 / c.272A>T / VUS / 48% / 163 / 1908 / 0.00% / AT rich region
MSH2 / NM_000251 / c.304G>A / VUS / 45% / 183 / 1913 / 0.00% / AT rich region
MSH2 / NM_000251 / c.319G>C / VUS / 58% / 67 / 986 / 0.00% / AT rich region
MSH2 / NM_000251 / c.362A>G / VUS / 36% / 140 / 1313 / 0.00% / AT rich region
MSH2 / NM_000251 / c.403C>T / VUS / 40% / 177 / 1531 / 0.00% / AT rich region
MSH2 / NM_000251 / c.557A>G / VUS / 43% / 138 / 1583 / 0.02%
MSH2 / NM_000251 / c.688G>C / VUS / 44% / 253 / 2495 / 0.00% / AT rich region
MSH2 / NM_000251 / c.707A>G / VUS / 51% / 199 / 2511 / 0.00%
MSH2 / NM_000251 / c.815C>T / VUS / 43% / 185 / 1718 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 39% / 251 / 2002 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 52% / 177 / 1904 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 42% / 254 / 2304 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 46% / 228 / 1956 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 42% / 85 / 636 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 45% / 272 / 2636 / 0.05% / AT rich region
MSH2 / NM_000251 / c.815C>T / VUS / 42% / 212 / 1943 / 0.05% / AT rich region
MSH2 / NM_000251 / c.835C>G / VUS / 44% / 217 / 2281 / 0.01% / AT rich region
MSH2 / NM_000251 / c.835C>G / VUS / 57% / 42 / 484 / 0.01% / AT rich region
MSH2 / NM_000251 / c.835C>G / VUS / 43% / 176 / 1408 / 0.01% / AT rich region
MSH2 / NM_000251 / c.942+3A>T / Mutation / 36% / 80 / 698 / 0.03% / Polymer stretch of 27As in 3' intron of Exon 5
MSH2 / NM_000251 / c.942+3A>T / Mutation / 56% / 59 / 949 / 0.03% / Polymer stretch of 27As in 3' intron of Exon 5
MSH2 / NM_000251 / c.942+3A>T / Mutation / 28% / 85 / 413 / 0.03% / Polymer stretch of 27As in 3' intron of Exon 5
MSH2 / NM_000251 / c.942+3A>T / Mutation / 37% / 90 / 633 / 0.03% / Polymer stretch of 27As in 3' intron of Exon 5
MSH2 / NM_000251 / c.942+3A>T / Mutation / 28% / 167 / 997 / 0.03% / Polymer stretch of 27As in 3' intron of Exon 5
MSH2 / NM_000251 / c.944G>T / VUS / 50% / 217 / 2103 / 0.01%
MSH2 / NM_000251 / c.964G>A / VUS / 46% / 94 / 817 / 0.01%
MSH2 / NM_000251 / c.968C>T / VUS / 44% / 133 / 1214 / 0.00%
MSH2 / NM_000251 / c.1035G>A / Mutation / 49% / 232 / 2573 / 0.00%
MSH2 / NM_000251 / c.1045C>G / VUS / 46% / 131 / 1276 / 0.01%
MSH2 / NM_000251 / c.1216C>T / Mutation / 42% / 173 / 1771 / 0.00%
MSH2 / NM_000251 / c.1327C>G / VUS / 37% / 169 / 1273 / 0.00% / AT rich region
MSH2 / NM_000251 / c.1561T>A / VUS / 48% / 181 / 2057 / 0.00%
MSH2 / NM_000251 / c.1709A>G / VUS / 46% / 83 / 816 / 0.00% / AT rich region
MSH2 / NM_000251 / c.1748A>G / VUS / 41% / 109 / 1136 / 0.01% / AT rich region
MSH2 / NM_000251 / c.1759+1G>A / VLP / 50% / 144 / 1886 / 0.00% / AT rich region
MSH2 / NM_000251 / c.1765G>A / VUS / 50% / 163 / 1804 / 0.00% / AT rich region
MSH2 / NM_000251 / c.1906G>C / Mutation / 47% / 72 / 856 / 0.01% / AT rich region
MSH2 / NM_000251 / c.1943T>A / VUS / 38% / 175 / 1187 / 0.00% / AT rich region
MSH2 / NM_000251 / c.2558A>C / VUS / 48% / 214 / 2244 / 0.00%
MSH2 / NM_000251 / c.2576_2584DELAATCGCAAG / VUS / 43% / 169 / 2630 / 0.01%
MSH2 / NM_000251 / c.2584G>A / VUS / 41% / 69 / 698 / 0.00%
MSH2 / NM_000251 / c.2714C>T / VUS / 47% / 210 / 2338 / 0.01% / AT rich region
MSH2 / NM_000251 / c.2714C>T / VUS / 45% / 83 / 736 / 0.01% / AT rich region
MSH2 / NM_000251 / c.2717T>C / VUS / 46% / 225 / 2310 / 0.00% / AT rich region
MSH2 / NM_000251 / c.2798C>T / VUS / 43% / 99 / 1086 / 0.00% / AT rich region
MSH2 / NM_000251 / c.2801C>T / VUS / 37% / 224 / 1893 / 0.00% / AT rich region
MUTYH / NM_001128425 / c.17C>A / VUS / 43% / 122 / 943 / 0.00% / GC rich region
MUTYH / NM_001128425 / c.536A>G / Mutation / 49% / 51 / 575 / 0.24%
MUTYH / NM_001128425 / c.700G>A / VUS / 41% / 99 / 827 / 0.03%
MUTYH / NM_001128425 / c.1187G>A / Mutation / 58% / 57 / 766 / 0.71% / GC rich region
MUTYH / NM_001128425 / c.1187G>A / Mutation / 54% / 68 / 844 / 0.71% / GC rich region
MUTYH / NM_001128425 / c.1187G>A / Mutation / 37% / 132 / 869 / 0.71% / GC rich region
MUTYH / NM_001128425 / c.1187G>A / Mutation / 47% / 49 / 590 / 0.71% / GC rich region
MUTYH / NM_001128425 / c.1187G>A / Mutation / 49% / 69 / 829 / 0.71% / GC rich region
MUTYH / NM_001128425 / c.1187G>A / Mutation / 55% / 97 / 1190 / 0.71% / GC rich region
NF1 / NM_001042492 / c.694A>T / VUS / 27% / 11 / 73 / 0.00% / AT rich region
PMS2 / NM_000535 / c.166C>G / VUS / 17% / 18 / 37 / 0.02% / AT rich region
POLE / NM_006231 / c.1A>T / VUS / 45% / 173 / 1645 / 0.00% / GC rich region
POLE / NM_006231 / c.902A>G / VUS / 42% / 153 / 1466 / 0.00%
POLE / NM_006231 / c.940T>G / VUS / 46% / 92 / 860 / 0.01%
POLE / NM_006231 / c.1019A>T / VUS / 55% / 126 / 1665 / 0.00%
POLE / NM_006231 / c.1171_1173DELAAG / VUS / 44% / 72 / 1166 / 0.00% / GC rich region
POLE / NM_006231 / c.1280C>T / VUS / 55% / 157 / 1820 / 0.00%
POLE / NM_006231 / c.3672_3674DUPAGC / VUS / 58% / 43 / 957 / 0.00%
PTEN / NM_000314 / c.-1243G>A / VUS / 51% / 102 / 1106 / 0.02%
PTEN / NM_000314 / c.-921G>A / VUS / 48% / 118 / 1283 / 0.01% / GC rich region
PTEN / NM_000314 / c.-976G>A / VUS / 69% / 13 / 155 / 0.09% / GC rich region
PTEN / NM_000314 / c.235G>A / VUS / 33% / 89 / 432 / 0.03% / AT rich region
PTEN / NM_000314 / c.235G>A / VUS / 35% / 175 / 1147 / 0.03% / AT rich region
PTEN / NM_000314 / c.235G>A / VUS / 41% / 163 / 1330 / 0.03% / AT rich region
PTEN / NM_000314 / c.509G>T / Mutation / 37% / 163 / 1215 / 0.00% / AT rich region
PTEN / NM_000314 / c.882T>G / VUS / 54% / 110 / 1256 / 0.01% / AT rich region
PTEN / NM_000314 / c.923G>A / VUS / 45% / 100 / 1006 / 0.00% / AT rich region
PTEN / NM_000314 / c.935A>G / VUS / 54% / 89 / 1162 / 0.00% / AT rich region
RAD50 / NM_005732 / c.1759A>C / VUS / 25% / 24 / 125 / 0.00% / AT rich region
RAD50 / NM_005732 / c.3230G>A / VUS / 17% / 36 / 65 / 0.01% / AT rich region
RAD51D / NM_002878 / c.26G>C / VUS / 45% / 82 / 888 / 0.08% / GC rich region
RAD51D / NM_002878 / c.146C>T / VUS / 36% / 173 / 1210 / 0.04%
RAD51D / NM_002878 / c.363DELA / Mutation / 52% / 31 / 516 / 0.00%
RAD51D / NM_002878 / c.434G>A / VUS / 14% / 586 / 998 / 0.01% / Mosaic variant
RAD51D / NM_002878 / c.607G>A / VUS / 45% / 121 / 1160 / 0.00%
1