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 computer assertion could be determined for this classification!


Variant: NM_000059.4(BRCA2):c.8168A>C (p.Asp2723Ala)

CA025483

52516 (ClinVar)

Gene: BRCA2
Condition: BRCA2-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 4ba6ceec-f98a-4a5b-8b20-b69a86adda01
Approved on: 2024-06-12
Published on: 2024-06-12

HGVS expressions

NM_000059.4:c.8168A>C
NM_000059.4(BRCA2):c.8168A>C (p.Asp2723Ala)
NC_000013.11:g.32363370A>C
CM000675.2:g.32363370A>C
NC_000013.10:g.32937507A>C
CM000675.1:g.32937507A>C
NC_000013.9:g.31835507A>C
NG_012772.3:g.52891A>C
ENST00000470094.2:c.8168A>C
ENST00000528762.2:c.8168A>C
ENST00000530893.7:c.7799A>C
ENST00000665585.2:c.8168A>C
ENST00000666593.2:c.8168A>C
ENST00000700202.2:c.8168A>C
ENST00000700202.1:c.635A>C
ENST00000380152.8:c.8168A>C
ENST00000544455.6:c.8168A>C
ENST00000614259.2:c.8176A>C
ENST00000665585.1:c.733A>C
ENST00000680887.1:c.8168A>C
ENST00000380152.7:c.8168A>C
ENST00000544455.5:c.8168A>C
NM_000059.3:c.8168A>C
More

Pathogenic

Met criteria codes 3
PS3 PP3 PP1_Strong
Not Met criteria codes 5
BA1 BS1 BP5 PP4 PM2

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.8168A>C variant in BRCA2 is a missense variant predicted to cause substitution of Aspartic acid by Alanine at amino acid 2723 (p.Asp2723Ala). This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met). This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.576, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. SpliceAI predictor score of 0.00 suggests that the variant has no impact on splicing (score threshold <0.10) (PP3 met). Reported by two calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs: 33609447, 33293522) (PS3 met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.557 (based on Pathology LR=0.214; Co-occurrence LR=1.102; Family History LR=2.36), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; 31853058, Internal lab contributors). Cosegregation analysis of family(ies) carrying this variant provided evidence towards pathogenicity, and has a Bayes Score of 74321.3, above the thresholds for Very strong pathogenic evidence (LR >350) (PP1_Very strong; Internal lab contributors). In summary, this variant meets the criteria to be classified as a Pathogenic variant variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PP3, PS3, PP1_Very strong).
Met criteria codes
PS3
Reported by two calibrated studies to exhibit protein function similar to pathogenic control variants (PMIDs: 33609447, 33293522) (PS3 met).

PP3
This BRCA2 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.576, above the recommended threshold of 0.30 for prediction of impact on BRCA2 function via protein change. SpliceAI predictor score of 0.00 suggests that the variant has no impact on splicing (score threshold <0.10) (PP3 met).
PP1_Strong
Cosegregation analysis of family(ies) carrying this variant provided evidence towards pathogenicity, and has a Bayes Score of 74321.3, above the thresholds for Very strong pathogenic evidence (LR >350) (PP1_Very strong; Internal lab contributors).
Not Met criteria codes
BA1
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
BS1
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
BP5
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.557 (based on Pathology LR=0.214; Co-occurrence LR=1.102; Family History LR=2.36), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; Internal lab contributors).
PP4
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.557 (based on Pathology LR=0.214; Co-occurrence LR=1.102; Family History LR=2.36), which is above the ENIGMA BRCA1/2 VCEP threshold for BP5 (>0.48) and below PP4 (<2.08) (BP5 and PP4 not met; Internal lab contributors).
PM2
This variant is present in gnomAD v2.1 (exomes only, non-cancer subset) or gnomAD v3.1 (non-cancer subset) but is below the ENIGMA BRCA1/2 VCEP threshold >0.00002 for BS1_Supporting (PM2_Supporting, BS1, and BA1 are not met).
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.