Table 2. Germline SNPs in TP53, STK11, ALK, APC, MSH2, MLH1, and CDH1 genes of 107 Korean gastric cancer patients.
| Sample | Chromosome | Start | End | Ref | Alter | Gene | Transcript ID | Amino acid change | Total depth | VAF(%)(1)a | VAF (%)(2)b | Clinical significance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| YMC 54 | 2 | 29449820 | 29449820 | G | A | ALK | NM_004304.4 | p.T1012M | 637 | 48.51% | 60.36% | Benign |
| YMC 7 | 2 | 29449820 | 29449820 | G | A | ALK | NM_004304.4 | p.T1012M | 208 | 55.77% | 43.83% | Benign |
| YMC 70 | 2 | 29449820 | 29449820 | G | A | ALK | NM_004304.4 | p.T1012M | 755 | 52.58% | 57.85% | Benign |
| SKW 18 | 2 | 29519923 | 29519923 | G | A | ALK | NM_004304.4 | p.L550F | 155 | 38.06% | 55.39% | VUS |
| YMC 13 | 5 | 112177778 | 112177778 | A | C | APC | NM_001127511.2 | p.K2145Q | 151 | 52.32% | 33.74% | Benign |
| YMC 24 | 5 | 112178865 | 112178865 | G | A | APC | NM_001127511.2 | p.R2507H | 1142 | 47.90% | 49.52% | VUS |
| SKW 38 | 5 | 112176548 | 112176548 | G | C | APC | NM_001127511.2 | p.A1735P | 628 | 45.86% | 47.30% | VUS |
| SKW 21 | 5 | 112173895 | 112173895 | A | C | APC | NM_001127511.2 | p.E850D | 147 | 55.78% | 50.93% | Benign |
| YMC 29 | 16 | 68867247 | 68867247 | G | A | CDH1 | NM_004360.4 | p.V832M | 1337 | 52.21% | 49.75% | Likely pathogenic |
| YMC 37 | 16 | 68867247 | 68867247 | G | A | CDH1 | NM_004360.4 | p.V832M | 1498 | 50.73% | 46.41% | Likely pathogenic |
| SKW 16 | 16 | 68856080 | 68856080 | C | G | CDH1 | NM_004360.4 | p.L630V | 928 | 43.74% | 40.61% | Benign |
| SKW 15 | 16 | 68856080 | 68856080 | C | G | CDH1 | NM_004360.4 | p.L630V | 827 | 49.33% | 71.46% | Benign |
| YMC 53 | 3 | 37053562 | 37053562 | C | T | MLH1 | NM_000249.3 | p.R217C | 1397 | 46.96% | 50.40% | VUS |
| YMC 55 | 3 | 37042521 | 37042521 | T | G | MLH1 | NM_000249.3 | p.S95A | 233 | 39.06% | 30.52% | VUS |
| YMC 6 | 3 | 37067240 | 37067240 | T | A | MLH1 | NM_000249.3 | p.V384D | 578 | 48.79% | 44.85% | Benign |
| YMC 70 | 3 | 37067240 | 37067240 | T | A | MLH1 | NM_000249.3 | p.V384D | 547 | 51.55% | 47.99% | Benign |
| YMC 14 | 3 | 37053562 | 37053562 | C | T | MLH1 | NM_000249.3 | p.R217C | 1409 | 45.71% | 51.65% | VUS |
| YMC 22 | 3 | 37067240 | 37067240 | T | A | MLH1 | NM_000249.3 | p.V384D | 862 | 99.54% | 100% | Benign |
| YMC 3 | 3 | 37090506 | 37090506 | C | A | MLH1 | NM_000249.3 | p.Q701K | 369 | 51.49% | 41.29% | Benign |
| YMC 4 | 3 | 37089022 | 37089022 | C | G | MLH1 | NM_000249.3 | p.L582V | 364 | 48.63% | 57.47% | VUS |
| YMC 37 | 3 | 37053562 | 37053562 | C | T | MLH1 | NM_000249.3 | p.R217C | 1315 | 49.20% | 49.76% | VUS |
| YMC 48 | 3 | 37067240 | 37067240 | T | A | MLH1 | NM_000249.3 | p.V384D | 899 | 43.38% | 44.61% | Benign |
| SKW 31 | 3 | 37053562 | 37053562 | C | T | MLH1 | NM_000249.3 | p.R217C | 294 | 55.78% | 39.71% | VUS |
| YMC 66 | 2 | 47656972 | 47656972 | C | T | MSH2 | NM_000251.2 | p.L390F | 197 | 56.85% | 52.78% | Benign |
| YMC 15 | 2 | 47656972 | 47656972 | C | T | MSH2 | NM_000251.2 | p.L390F | 1281 | 46.68% | 79.62% | Benign |
| YMC 28 | 2 | 47630344 | 47630344 | C | A | MSH2 | NM_000251.2 | p.P5Q | 231 | 53.25% | 86.79% | VUS |
| YMC 5 | 2 | 47637371 | 47637371 | A | G | MSH2 | NM_000251.2 | p.I169V | 711 | 51.34% | 45.12% | Likely benign |
| YMC 48 | 2 | 47656972 | 47656972 | C | T | MSH2 | NM_000251.2 | p.L390F | 692 | 51.30% | 53.31% | Benign |
| SKW 41 | 2 | 47703564 | 47703564 | G | A | MSH2 | NM_000251.2 | p.M688I | 993 | 52.57% | 50.83% | VUS |
| SKW 40 | 17 | 7578209 | 7578209 | G | A | TP53 | NM_000546.5 | p.H214Y | 168 | 39.29% | 59.58% | VUS |
a, tumor tissue; b, matched non-tumor tissue.
Abbreviation: Ref, reference allele; Alter, Altered allele; VAF, Variant allele frequency; VUS, a variant of unknown significance.