Table 2 Distribution of PathoMAN reclassified germline cancer variants by variant class
From: Toward automation of germline variant curation in clinical cancer genetics
Variant class | Description | Reported B/LB | Reported P/LP | Reported VUS | Total | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
B/LB | P/LP | VUS | B/LB | P/LP | VUS | B/LB | P/LP | VUS | |||
3PU | Variant in 3′ untranslated region | 0 | 0 | 3 | 0 | 0 | 3 | 0 | 0 | 7 | 13 |
5PU | Variant in 5′ untranslated region | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 5 |
EE | Variant that alters the first or last 3 bases of an exon, but not the frame of the coding sequence | 6 | 0 | 13 | 0 | 17 | 0 | 2 | 2 | 46 | 86 |
ESS | 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 | In-frame 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 | Stopgain (nonsense) variant caused by base substitution | 0 | 0 | 2 | 0 | 161 | 0 | 0 | 0 | 1 | 164 |
SS | Variant that alters splice-site within the first 8 intronic bases flanking exon but not an ESS or SS5 | 17 | 0 | 3 | 1 | 4 | 3 | 1 | 0 | 56 | 85 |
SS5 | 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 | Â | 1020 | 0 | 238 | 2 | 568 | 32 | 63 | 26 | 1565 | 3513 |
