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 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.631+4A>G

CA023861

52056 (ClinVar)

Gene: BRCA2 (HGNC:675)
Condition: BRCA2-related cancer predisposition (MONDO:0700269)
Inheritance Mode: Autosomal dominant inheritance
UUID: c606ba33-bde7-4122-bd73-7cd241b13573
Approved on: 2025-08-18
Published on: 2025-08-18

HGVS expressions

NM_000059.4(BRCA2):c.631+4A>G
NM_000059.4:c.631+4A>G
NC_000013.11:g.32326617A>G
CM000675.2:g.32326617A>G
NC_000013.10:g.32900754A>G
CM000675.1:g.32900754A>G
NC_000013.9:g.31798754A>G
NG_012772.3:g.16138A>G
ENST00000470094.2:c.631+4A>G
ENST00000528762.2:c.631+4A>G
ENST00000530893.7:c.262+4A>G
ENST00000665585.2:c.631+4A>G
ENST00000666593.2:c.631+4A>G
ENST00000700202.2:c.631+4A>G
ENST00000700200.1:n.506A>G
ENST00000700201.1:c.*410+4A>G
ENST00000380152.8:c.631+4A>G
ENST00000544455.6:c.631+4A>G
ENST00000614259.2:c.631+4A>G
ENST00000680887.1:c.631+4A>G
ENST00000380152.7:c.631+4A>G
ENST00000530893.6:n.829+4A>G
ENST00000544455.5:c.631+4A>G
ENST00000614259.1:n.631+4A>G
NM_000059.3:c.631+4A>G
More

Likely Pathogenic

Met criteria codes 2
PM2 PVS1
Not Met criteria codes 1
PP3

Evidence Links 0

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.631+4A>G variant is an intronic variant occurring in intron 7 of the BRCA2 gene. 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 intronic variant is located outside of the native donor and acceptor 1,2 splice sites, and has a SpliceAI score of 0.71, predicting an impact on splicing (score threshold ≥0.2) (PP3 not applied because a PVS1 code is met). This variant is reported to result in aberrant mRNA splicing. RNAseq, minigene and RT-PCR demonstrated that the variant impacts splicing by exon skipping (PMIDs: 20455026, 31143303). Preliminary code strength determined by comparison of results to PVS1 decision tree and assessment of mRNA splicing data (PVS1 (RNA) met). The percent reference (full-length, FL) and aberrant transcripts produced from the variant allele using allele specific quantitative assessment with Capillary electrophoresis was determined to be full-length (0%) / exon skipping (100%). Final code strength determined by the rubric: PVS1 (RNA). 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 (PM2_Supporting, PVS1 (RNA)).
Met criteria codes
PM2
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).
PVS1
This variant is reported to result in aberrant mRNA splicing. RNAseq, minigene and RT-PCR demonstrated that the variant impacts splicing by exon skipping (PMIDs: 20455026, 31143303). Preliminary code strength determined by comparison of results to PVS1 decision tree and assessment of mRNA splicing data (PVS1 (RNA) met). The percent reference (full-length, FL) and aberrant transcripts produced from the variant allele using allele specific quantitative assessment with Capillary electrophoresis was determined to be full-length (0%) / exon skipping (100%). Final code strength determined by the rubric: PVS1 (RNA).
Not Met criteria codes
PP3
This BRCA2 intronic variant is located outside of the native donor and acceptor 1,2 splice sites, and has a SpliceAI score of 0.71, predicting an impact on splicing (score threshold ≥0.2) (PP3 not applied because a PVS1 code is met).
Curation History
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