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.7795G>A (p.Glu2599Lys)

CA10579756

231552 (ClinVar)

Gene: BRCA2 (HGNC:675)
Condition: BRCA2-related cancer predisposition (MONDO:0700269)
Inheritance Mode: Autosomal dominant inheritance
UUID: d8d6156d-eee3-464f-81ed-1387c699ac19
Approved on: 2026-08-28
Published on: 2026-08-27

HGVS expressions

NM_000059.4(BRCA2):c.7795G>A (p.Glu2599Lys)
NM_000059.4:c.7795G>A
NC_000013.11:g.32357919G>A
CM000675.2:g.32357919G>A
NC_000013.10:g.32932056G>A
CM000675.1:g.32932056G>A
NC_000013.9:g.31830056G>A
NG_012772.3:g.47440G>A
ENST00000470094.2:c.7795G>A
ENST00000528762.2:c.7795G>A
ENST00000530893.7:c.7426G>A
ENST00000665585.2:c.7795G>A
ENST00000666593.2:c.7795G>A
ENST00000700202.2:c.7795G>A
ENST00000700202.1:c.262G>A
ENST00000380152.8:c.7795G>A
ENST00000544455.6:c.7795G>A
ENST00000614259.2:c.7795G>A
ENST00000665585.1:c.360G>A
ENST00000680887.1:c.7795G>A
ENST00000380152.7:c.7795G>A
ENST00000544455.5:c.7795G>A
ENST00000614259.1:n.7795G>A
NM_000059.3:c.7795G>A
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Likely Pathogenic

Met criteria codes 3
PM2_Supporting PS3 PM3_Supporting
Not Met criteria codes 4
BP4 BP1 PP4 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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.7795G>A variant in BRCA2 is a missense variant predicted to cause substitution of Glutamic Acid by Lysine at amino acid 2599 (p.(Glu2599Lys)). This variant is absent from gnomAD v4.1 (read depth ≥25x in >90% samples, PM2_Supporting met). Reported by three calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs:38417439, 39779857, 39779848) (PS3 met). This BRCA2 missense variant is within a key functional domain. The computational predictor BayesDel (noAF) gives a score of 0.25, indicating that impact on BRCA2 function via protein change is unclear (score range 0.18-0.30) and the SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score range 0.10-0.20) (no bioinformatic code is applied). This variant has been detected in an individual with phenotype suggestive of BRCA2-Fanconi Anemia (FA). Clinical features of FA (no details reported) and Mitomicin-C (MMC)-induced chromosomal damage are seen in this individual. They were compound heterozygous for the variant and a pathogenic or likely pathogenic variant (BRCA2:c.7890_7891dup, p.Leu2631HisfsTer18) inferred to be in trans, phase was unknown. Total points equated to 1 (PM3_Supporting met; PMID: 23285130). 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, PS3, PM3_Supporting).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1 (read depth ≥25x in >90% samples, PM2_Supporting met).
PS3
Reported by three calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs:38417439, 39779857, 39779848) (PS3 met).
PM3_Supporting
This variant has been detected in an individual with phenotype suggestive of BRCA2-Fanconi Anemia (FA). Clinical features of FA (no details reported) and Mitomicin-C (MMC)-induced chromosomal damage are seen in this individual. They were compound heterozygous for the variant and a pathogenic or likely pathogenic variant (BRCA2:c.7890_7891dup, p.Leu2631HisfsTer18) inferred to be in trans, phase was unknown. Total points equated to 1 (PM3_Supporting met; PMID: 23285130).
Not Met criteria codes
BP4
This BRCA2 missense variant is within a key functional domain. The computational predictor BayesDel (noAF) gives a score of 0.25, indicating that impact on BRCA2 function via protein change is unclear (score range 0.18-0.30) and the SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score range 0.10-0.20) (no bioinformatic code is applied).
BP1
This BRCA2 missense variant is within a key functional domain. The computational predictor BayesDel (noAF) gives a score of 0.25, indicating that impact on BRCA2 function via protein change is unclear (score range 0.18-0.30) and the SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score range 0.10-0.20) (no bioinformatic code is applied).
PP4
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1 (based on Case-Control LR=1), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; PMID: 40413188).
PP3
This BRCA2 missense variant is within a key functional domain. The computational predictor BayesDel (noAF) gives a score of 0.25, indicating that impact on BRCA2 function via protein change is unclear (score range 0.18-0.30) and the SpliceAI score of 0.17 indicates an unclear predicted impact on splicing (score range 0.10-0.20) (no bioinformatic code is applied).
Curation History
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