Table 2:
Distribution of PathoMAN re-classified of expertly curated germline cancer variants by variant class
| Variant Class | Description | Reported BLB | Reported PLP | Reported VUS | Total | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| BLB | PLP | VUS | BLB | PLP | VUS | BLB | PLP | VUS | |||
| 3PU | Any variant in 3′ untranslated region | 0 | 0 | 3 | 0 | 0 | 3 | 0 | 0 | 7 | 13 |
| 5PU | Any variant in 5′ untranslated region | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 5 |
| EE | Variant that alters the first or last three bases of an exon (i.e., the exon end), but not the frame of the coding sequence | 6 | 0 | 13 | 0 | 17 | 0 | 2 | 2 | 46 | 86 |
| ESS | Any variant that alters essential splice-site base (+1, +2, −1, −2) | 0 | 0 | 0 | 0 | 51 | 0 | 1 | 3 | 2 | 57 |
| FS | Frameshifting insertion and/or deletion. It alters length and frame of coding sequence | 0 | 0 | 1 | 0 | 252 | 1 | 0 | 2 | 7 | 263 |
| IF | Inframe insertion and/or deletion. It alters length but not frame of coding sequence | 1 | 0 | 4 | 0 | 8 | 0 | 0 | 1 | 31 | 45 |
| IM | Variant that alters initiating methionine start codon | 0 | 0 | 0 | 0 | 3 | 2 | 0 | 0 | 4 | 9 |
| NSY | Nonsynonymous variant. It alters amino acid(s) but not coding sequence length | 169 | 0 | 211 | 0 | 71 | 22 | 19 | 17 | 1395 | 1904 |
| SG | Stop-gain (nonsense) variant caused by base substitution | 0 | 0 | 2 | 0 | 161 | 0 | 0 | 0 | 1 | 164 |
| SS | Any variant that alters splice-site base within the first eight intronic bases flanking exon (i.e., +8 to −8) but not an ESS or SS5 base | 17 | 0 | 3 | 1 | 4 | 3 | 1 | 0 | 56 | 85 |
| SS5 | Any variant that alters +5 splice-site base but not an ESS base | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 11 | 15 |
| SY | Synonymous variant. It does not alter amino acid or coding sequence length | 826 | 0 | 0 | 1 | 0 | 0 | 40 | 0 | 0 | 867 |
| Total | 1020 | 0 | 238 | 2 | 568 | 32 | 63 | 26 | 1565 | 3513 | |