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Table 2 Sequence variants identified in the BRCA2 gene

From: Prevalance of BRCA1 and BRCA2 mutations in familial breast cancer patients in Lebanon

Nucleotide Change AA change Number of patients Clinical Relevance (BIC) Variation class§ Polyphen SIFT Align GVGD
Frameshift mutations
5804_5808delTTAA I1859KfsX3 1 Deleterious 5    
c.9485-1 G > A*   1 Not reported Not reported    
Missense variations
353A > G Y42C 1 Unknown 1 +++ Tolerated Class 0
1093A > C N289H 6 No effect 1 + Not tolerated Class 0
1342A > C N372H 20 No effect 1 + Tolerated Class 0
3199A > G N991D 2 Unknown 1 ++ Tolerated Class 0
5972 C > T T1915M 2 Unknown 1 ++ Tolerated Class 0
6359 G > C G2044A 1 Unknown 3 + Tolerated Class 0
6550 C > T R2108C 1 Unknown 3 +++ Tolerated Class 0
7625 C > T A2466V 26 Unknown 1 + Not tolerated Class 0
9079 G > A A2951T 1 No effect 2 + Not tolerated Class 55
Nonsense mutations
10204A > T K3326X 1 No effect 1    
Synonyms
1593A > G S455S 6 No effect 1    
2457 T > C H743H 6 Unknown 1    
3624A > G K1132K 16 No effect 1    
4035 T > C V1269V 13 No effect 1    
4791A > G L1521L 38 No effect 2    
5718 C > T S1830S 1 Not reported Not reported    
6741 C > G V2171V 38 Unknown 1    
7470A > G S2414S 13 No effect 1    
10338 G > A R3370R 1 Unknown 1    
UTRs and Intronic variations
203 G > A 5’UTR 16 No effect Not reported    
IVS4 + 67A > C   6 Unknown 1    
IVS4 + 147 G > T   4 Not reported Not reported    
IVS6 + 14 C > T   1 Unknown 3    
IVS7 + 183 T > A   21 Not reported 1    
IVS7-9A > G   1 Unknown Not reported    
IVS8 + 56 C > T   8 Unknown 1    
IVS10-34 C > A   1 Not reported 3    
IVS10-51 G > T   1 Not reported 1    
IVS11 + 80delTTAA   10 Unknown 3    
IVS12-120 T > C   37 Not reported 3    
IVS13 + 133insATTATAAAA   5 Not reported Not reported    
IVS13 + 273 G > A   2 Not reported Not reported    
IVS14 + 53 C > T   4 No effect Not reported    
IVS16-14 T > C   25 No effect 1    
IVS21-66 T > C   25 No effect 1    
IVS22 + 53 C > G   1 Not reported Not reported    
IVS24-16 T > C   1 Unknown 1    
10485 + 105A > C 3’UTR 15 Not reported Not reported    
  1. *Missense considered deleterious.
  2. Polyphen: +++ Variant predicted to be probably damaging, ++ Variant predicted to be possibly damaging, + Variant predicted to be benign.
  3. UMD-BRCA1/2: 1 Variant considered neutral, 2 Variant considered likely-neutral, 3 Variant considered unclassified, 4 Variant considered likely-causal, 5 Variant considered causal.
  4. § in the UMD-BRCA1 database (http://www.umd.be/BRCA1/) (12) using classification system in five classes (13).