The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: BRCA2 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000059.4(BRCA2):c.7857G>C (p.Trp2619Cys)

CA387747060

438744 (ClinVar)

Gene: BRCA2
Condition: BRCA2-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 4c506160-1353-4a2b-9c8f-f9ea4e682aff
Approved on: 2025-05-23
Published on: 2025-05-23

HGVS expressions

NM_000059.4:c.7857G>C
NM_000059.4(BRCA2):c.7857G>C (p.Trp2619Cys)
NC_000013.11:g.32362574G>C
CM000675.2:g.32362574G>C
NC_000013.10:g.32936711G>C
CM000675.1:g.32936711G>C
NC_000013.9:g.31834711G>C
NG_012772.3:g.52095G>C
ENST00000470094.2:c.7857G>C
ENST00000528762.2:c.7857G>C
ENST00000530893.7:c.7488G>C
ENST00000665585.2:c.7857G>C
ENST00000666593.2:c.7857G>C
ENST00000700202.2:c.7857G>C
ENST00000700202.1:c.324G>C
ENST00000380152.8:c.7857G>C
ENST00000544455.6:c.7857G>C
ENST00000614259.2:c.7865G>C
ENST00000665585.1:c.422G>C
ENST00000680887.1:c.7857G>C
ENST00000380152.7:c.7857G>C
ENST00000544455.5:c.7857G>C
ENST00000614259.1:n.7865G>C
NM_000059.3:c.7857G>C
More

Likely Pathogenic

Met criteria codes 3
PM2_Supporting PS3 PP3
Not Met criteria codes 2
BP5 PP4

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRCA2 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The variant c.7857G>C in BRCA2 is a missense variant predicted to cause substitution of Tryptophan by Cysteine at amino acid 2619 (p.Trp2619Cys). This variant is absent from gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥25) and gnomAD v3.1 (non-cancer subset, read depth ≥25) (PM2_Supporting met). This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.49, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. A SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score threshold 0.10-0.20) (PP3 met). Reported by four calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs: 38417439, 32444794, 39779857, 39779848) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1.81 (based on Family History LR=1.81), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; PMIDs 31853058). In summary, this variant meets the criteria to be classified as a likely pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PS3, PM2_Supporting, PP3).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥25) and gnomAD v3.1 (non-cancer subset, read depth ≥25) (PM2_Supporting met).
PS3
Reported by four calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs: 38417439, 32444794, 39779857, 39779848) (PS3 met).

PP3
This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.49, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. A SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score threshold 0.10-0.20) (PP3 met).
Not Met criteria codes
BP5
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1.81 (based on Family History LR=1.81), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; PMIDs 31853058).
PP4
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1.81 (based on Family History LR=1.81), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; PMIDs 31853058). Li et al, 2020, (PMID: 31853058): log(LR)=0.257565, 1 proband --> LR=1.81
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.