Table 4. Predicted effect of 12 VUS in BRCA1 and BRCA2 and effects at RNA level.
| Variant | Predicted effect In silico | Predicted effect Alamut | VUS classification before RNAa | Evidence to support classification | Abnormal splicing on RNA | Effect on RNA |
|---|---|---|---|---|---|---|
| BRCA1c.4676-7C>T | No significant change predicted | N/A | Class 2 | Published data based on a multifactorial likelihood-ratio model predicts it to be neutral | No | None |
| BRCA1 c.4868C>G p.(Ala1623Gly) | Strong effect predicted (creation of cryptic novel high ranking splice-acceptor site) | Amino acid not evolutionary conserved | Class 5 | From previous published evidence of effect on splicing | Yes | Heterozygous deletion in exon 15 r.4868_4986del (NM_007294.3 on Ensembl) |
| BRCA1 c.5152+4A>G | Strong effect predicted (significant reduction in splice donor ranking plus creation of novel splice donor and acceptor) | N/A | Class 3 | Yes | Heterozygous deletion of exon 17 r.5075_5152del (NM_007294.3 on Ensembl) | |
| BRCA2c.1395A>C, p.(=) | No significant change predicted (loss of cryptic splice acceptor) | N/A | Class 1 | Range of published evidence including no effect on splicing | No | None |
| BRCA2c.4614T>C, p.(=) | No significant change predicted | N/A | Class 1 | Good co-occurrence data | No | None |
| BRCA2c.5319G>C, p.(Glu1773Asp) | No significant change predicted | Amino acid not evolutionary conserved | Class 3 | No | None | |
| BRCA2c.6725A>T, p.(Asp2242Val) | No significant change predicted | Amino acid conserved, change not predicted as disruptive | Class 3 | No | None | |
| BRCA2 c.7540A>G, p.(Lys2514Glu) | Moderate effect (3/5 predict new splice donor) | Amino acid conserved change predicted disruptive | Class 3 | No | None | |
| BRCA2c.7939C>G, p.(Leu2647Val) | Moderate effect (3/5 predict new splice donor) | Amino acid conserved, change predicted disruptive (2/3) | Class 3 | No | None | |
| BRCA2c.8488-5T>C | Moderate effect (reduction in ranking of splice acceptor) | N/A | Class 3 | No | None | |
| BRCA2c.6750A>G, p.(=) | No significant change predicted | N/A | Class 3 | No | None | |
| BRCA2c.9082G>C, p.(Ala3028Pro) | No significant change predicted | Amino acid not evolutionary conserved, change not predicted disruptive | Class 3 | No | None |
Reference sequences used: LRG_292t1 (BRCA1); LRG_293t1 (BRCA2).
Submission to LOVD: http://databases.lovd.nl/shared/genes/BRCA1
BRCA1 c.4676-7C>T Submission of screening #0000063401.
BRCA1 c.4868C>G p.(Ala1623Gly) Submission of screening #0000063402.
BRCA1 c.5152+4A>G Submission of screening #0000063403.
BRCA2 c.1395A>C, p.(=) Submission of screening #0000063404.
BRCA2 c.4614T>C, p.(=) Submission of screening #0000063405.
BRCA2 c.5319G>C, p.(Glu1773Asp) Submission of screening #0000063406.
BRCA2 c.6725A>T, p.(Asp2242Val) Submission of screening #0000063407.
BRCA2 c.7540A>G, p.(Lys2514Glu) Submission of screening #0000063414.
BRCA2 c.7939C>G, p.(Leu2647Val) Submission of screening #0000063417.
BRCA2 c.8488-5T>C Submission of screening #0000063422.
BRCA2 c.6750A>G, p.(=) Submission of screening #0000063427.
BRCA2 c.9082G>C, p.(Ala3028Pro) Submission of screening #0000063428.