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.7792GAA[1] (p.Glu2599del)

CA025277

52409 (ClinVar)

Gene: BRCA2 (HGNC:675)
Condition: BRCA2-related cancer predisposition (MONDO:0700269)
Inheritance Mode: Autosomal dominant inheritance
UUID: 41597833-4998-4a1f-ae06-ff349b2c6c89
Approved on: 2026-09-21
Published on: 2026-09-21

HGVS expressions

NM_000059.4(BRCA2):c.7792GAA[1] (p.Glu2599del)
NM_000059.4:c.7792GAA[1]
NM_000059.4:c.7795_7797del
NC_000013.11:g.32357919_32357921del
CM000675.2:g.32357919_32357921del
NC_000013.10:g.32932056_32932058del
CM000675.1:g.32932056_32932058del
NC_000013.9:g.31830056_31830058del
NG_012772.3:g.47440_47442del
ENST00000470094.2:c.7795_7797del
ENST00000528762.2:c.7795_7797del
ENST00000530893.7:c.7426_7428del
ENST00000665585.2:c.7795_7797del
ENST00000666593.2:c.7795_7797del
ENST00000700202.2:c.7795_7797del
ENST00000700202.1:c.262_264del
ENST00000380152.8:c.7795_7797del
ENST00000544455.6:c.7795_7797del
ENST00000614259.2:c.7795_7797del
ENST00000665585.1:c.360_362del
ENST00000680887.1:c.7795_7797del
ENST00000380152.7:c.7795_7797del
ENST00000544455.5:c.7795_7797del
ENST00000614259.1:n.7795_7797del
NM_000059.3:c.7795_7797del
More

Likely Pathogenic

Met criteria codes 2
PP4_Strong PP3
Not Met criteria codes 4
BS1 BP7 BA1 PM2

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.7795_7797del variant in BRCA2 is predicted to cause a change in the length of the protein due to an in-frame deletion of 1 amino acid (p.(Glu2599del)). The Total GrpMax filtering allele frequency (the lower threshold of the 95% CI) in gnomAD v4.1 is 0.00000028 in the Non-Finnish European genetic ancestry group (based on 2/1179946 alleles) which is below the ENIGMA BRCA1/2 VCEP threshold (>0.00002) for BS1_Supporting and does not meet any population code (BA1, BS1, BS1_Supporting, PM2_Supporting are not met). This BRCA2 in-frame deletion variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.64, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. A SpliceAI score of 0.03 predicts no impact on splicing (score threshold ≤0.1) (PP3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 2883172307.4 (based on Cosegregation LR=10545472; Pathology LR=0.93; Co-occurrence LR=1.03; Family History LR=285.42), above the thresholds for very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 34597585, 31853058, 31131967). This is an in-frame variant inside a key functional domain. Impact via the protein change has not been assessed yet. mRNA experimental analysis indicates no impact on splicing (PMIDs: 22505045, 27886673) but is not applied as strong evidence against pathogenicity since missense impact has not been excluded (BP7_Strong (RNA) not met). 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 (PP3, PP4_Very strong).
Met criteria codes
PP4_Strong
at Very strong level: Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 2883172307.4 (based on Cosegregation LR=10545472; Pathology LR=0.93; Co-occurrence LR=1.03; Family History LR=285.42), above the thresholds for very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 34597585, 31853058, 31131967).
PP3
This BRCA2 in-frame deletion variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.64, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. A SpliceAI score of 0.03 predicts no impact on splicing (score threshold ≤0.1) (PP3 met).
Not Met criteria codes
BS1
The Total GrpMax filtering allele frequency (the lower threshold of the 95% CI) in gnomAD v4.1 is 0.00000028 in the Non-Finnish European genetic ancestry group (based on 2/1179946 alleles) which is below the ENIGMA BRCA1/2 VCEP threshold (>0.00002) for BS1_Supporting and does not meet any population code (BA1, BS1, BS1_Supporting, PM2_Supporting are not met).
BP7
This is an in-frame variant inside a key functional domain. Impact via the protein change has not been assessed yet. mRNA experimental analysis indicates no impact on splicing (PMIDs: 22505045, 27886673) but is not applied as strong evidence against pathogenicity since missense impact has not been excluded (BP7_Strong (RNA) not met).
BA1
The Total GrpMax filtering allele frequency (the lower threshold of the 95% CI) in gnomAD v4.1 is 0.00000028 in the Non-Finnish European genetic ancestry group (based on 2/1179946 alleles) which is below the ENIGMA BRCA1/2 VCEP threshold (>0.00002) for BS1_Supporting and does not meet any population code (BA1, BS1, BS1_Supporting, PM2_Supporting are not met).
PM2
The Total GrpMax filtering allele frequency (the lower threshold of the 95% CI) in gnomAD v4.1 is 0.00000028 in the Non-Finnish European genetic ancestry group (based on 2/1179946 alleles) which is below the ENIGMA BRCA1/2 VCEP threshold (>0.00002) for BS1_Supporting and does not meet any population code (BA1, BS1, BS1_Supporting, PM2_Supporting are not met).
Curation History
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