Table 2.
BRCA2 variants used to test the performance of the VarCall model.
| Varianta | Amino acid changeb | ClinVar classificationc | BRCA exchanged | mES-based classificatione |
|---|---|---|---|---|
| c.73G > A | p.Gly25Arg (G25R) | Uncertain (2) | Indeterminate | |
| c.91 T > C | p.TrpW31Arg (W31R) | Uncertain (1) | Non-functional | |
| c.93 G > T | p.Trp31Cys (W31C) | Likely Pathogenic (1)/Uncertain (1) | Non-functional | |
| c.73_118del (delex3-5’) | p.Gly25_Ala40del (G25_A40del) | Non-functional | ||
| c.119_312del (delex3-3’) | p.Pro41_Asp104del (P41_D104del) | Functional | ||
| c.317_631del (delex4-7) | p.Gly106_Ile210del (G106_I210del) | Indeterminate | ||
| c.581 G > A | p.Trp194Stop (W194X) | Pathogenic (10) | Pathogenic | Non-functional |
| c.631 + 2 T > G | IVS7 + 2 T > G | Pathogenic (2)/Likely Pathogenic (1) | Pathogenic | Non-functional |
| c.1964C > G | p.Pro655Arg (P655R) | Benign (22) | Benign | Functional |
| c.6323 G > A | p.Arg2108His (R2108H) | Benign (27) | Benign | Functional |
| c.6853 A > G | p.Ile2285Val (I2285V) | Benign (18) | Benign | Functional |
| c.6842_6937del (delex12) | p.Gly2281_Asp2312de (G2281_D2312del)l | Functional | ||
| c.7007 G > A | p.Arg2336His(R2336H) | Pathogenic (23) | Pathogenic | Functional |
| c.7216_7217TT > GA | p.Phe2406Asp (F2406D) | Functional | ||
| c.7218 T > G | p.Phe2406Leu (F2406L) | Uncertain (1) | Functional | |
| c.7468 A > G | p.Ile2490Thr (I2490T) | Uncertain (1) | Functional | |
| c.7529 T > C | p.Leu2510Pro (L2510P) | Likely Pathogenic (4) | Non-functional | |
| c.7878 G > C | p.Trp2626Cys(W2626C) | Pathogenic (16) | Pathogenic | Non-functional |
| c.7958 T > C | p.Leu2653Pro (L2653P) | Pathogenic (4)/Likely Pathogenic (3) | Non-functional | |
| c.8084 C > T | p.Ser2695Leu (S2695L) | Likely benign (1)/Uncertain (2) | Functional | |
| c.8187 G > T | p.Lys2729Asn (K2729N) | Benign (16) | Benign | Functional |
| c.8830 A > T | p.Iso2944Phe (I2944F) | Benign (26) | Benign | Functional |
| c.9004 G > A | p.Glu3002Lys (E3002K) | Pathogenic (11)/Likely Pathogenic (4) | Nonfunctional | |
| c.9285 C > G | p.Asp3095Glu (D3095E) | Pathogenic (6)/Likely Pathogenic (2) | Nonfunctional | |
| c.9371 A > T | p.Asn3124Iso (N3124I) | Pathogenic (20) | Pathogenic | Nonfunctional |
aVariant names are according to HGVS nomenclature.
bSingle letter amino acid codes are in the parentheses.
cNumber of entries in ClinVar as of 23rd September 2020 are in the parentheses.
dWebsite: https://brcaexchange.org/variants.
eVariants previously characterized by ES cell-based functional assay22–24.