Table 2.
Non-synonymous exonic variants not matched in CIViC and ClinVar with their OMIM phenotype and pathogenicity prediction
| Sample | Gene | Ref | Counts (%) | Alt | Counts (%) | Total reads | AA change | Hom /Het | OMIM phenotype and Mode of inheritance | S_P | P_P | MT_P |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GDN4252 | BCL10 | C | 49 (43%) | A | 64 (56%) | 114 | A5S | Het | Male germ cell tumor, somatic | T | B | N |
| GDN4253 | BCL10 | C | 28 (55%) | A | 23 (45%) | 51 | A5S | Het | Male germ cell tumor, somatic | T | B | N |
| BIRC3 | A | 28 (52%) | G | 26 (45%) | 54 | K260R | Het | – | T | B | N | |
| NOTCH1 | T | 16 (38%) | C | 26 (62%) | 42 | I567V | Het | – | T | B | D | |
| ATM | G | 112 (53%) | T | 99 (47%) | 211 | C1482F | Het | T-cell prolymphocytic leukemia, somatic | T | B | N | |
| GDN4255 | BCL10 | C | 58 (48%) | A | 62 (51%) | 121 | A5S | Het | Male germ cell tumor, somatic | T | B | N |
| NOTCH1 | A | 104 (75%) | T | 35 (25%) | 139 | V1699E | Het | – | D | D | D | |
| BIRC3 | A | 57 (55%) | G | 46 (45%) | 103 | K260R | Het | – | T | B | N | |
| ASXL1 | G | 90 (49%) | A | 95 (51%) | 185 | D1163N | Het | Myelodysplastic syndrome, somatic | T | B | N | |
| GDN4256 | BIRC3 | A | 14 (39%) | G | 22 (61%) | 36 | K260R | Het | – | T | B | N |
| GDN4258 | MUTYH | G | 35 (49%) | A | 37 (51%) | 72 | A230V | Het | – | T | P | D |
| KIT | A | 47 (44%) | G | 59 (56%) | 106 | I438V | Het | Germ cell tumors, somatic, Leukemia, acute myeloid (Smu,AD) | T | B | D | |
| ATM | A | 68 (46%) | G | 80 (54%) | 149 | H24R | Het | T-cell prolymphocytic leukemia, somatic | T | B | N | |
| ATM | C | 49 (49%) | T | 50 (51%) | 99 | H1380Y | Het | T-cell prolymphocytic leukemia, somatic | T | B | N | |
| SETBP1 | G | 14 (47%) | T | 16 (53%) | 30 | E1466D | Het | – | T | B | N | |
| GDN4259 | NOTCH 1 | C | 72 (43%) | T | 94 (56%) | 167 | V1232M | Het | – | T | P | N |
| ASXL1 | C | 51 (49%) | T | 53 (51%) | 104 | Q757X | Het | Myelodysplastic syndrome, somatic | T | 0 | D | |
| GDN4260 | MUTYH | C | 66 (55%) | T | 54 (45%) | 121 | G25D | Het | – | T | P | N |
| MUTYH | G | 55 (51%) | A | 52 (49%) | 107 | P18L | Het | – | T | B | D | |
| BCL10 | C | 0 (0%) | A | 57 (97%) | 59 | A5S | Hom | Male germ cell tumor, somatic | T | B | N | |
| GDN4261 | PTPN11 | T | 156 (83%) | C | 32 (17%) | 188 | S502P | Het | Leukemia, juvenile myelomonocytic, somatic | T | P | D |
| FLT3 | 11 (12%) | del and ins | 71 (78%) | 85 | YFY589-91delWAGDins | Het | ALL, AML | 0 | 0 | 0 | ||
| BCR | – | 44 (72) | CCGGins | 17 (27) | 61 | S1092fs | Het | ALL, CML somatic | 0 | 0 | 0 | |
| GDN4262 | ATM | A | 107 (54%) | C | 91 (46%) | 198 | T1697P | Het | T-cell prolymphocytic leukemia, somatic | T | B | N |
Ref Reference Allele, Alt Alternate Allele, Counts Read Counts, AA Change Amino acid Change, Hom/Het Homozygous/Heterozygous, S_P SIFT_Prediction, P_P PolyPhen2 Prediction and MT_P Mutation taster Prediction. B – Benign, D – Damaging, P – Probably Damaging, N – Neutral, T- Tolerated, 0 – No prediction