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.8023A>G (p.Ile2675Val)

CA025410

52475 (ClinVar)

Gene: BRCA2
Condition: BRCA2-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: a635e51b-a3d1-4c44-b83f-c8e9bad4ccaf
Approved on: 2024-06-12
Published on: 2024-06-12

HGVS expressions

NM_000059.4:c.8023A>G
NM_000059.4(BRCA2):c.8023A>G (p.Ile2675Val)
NC_000013.11:g.32363225A>G
CM000675.2:g.32363225A>G
NC_000013.10:g.32937362A>G
CM000675.1:g.32937362A>G
NC_000013.9:g.31835362A>G
NG_012772.3:g.52746A>G
ENST00000470094.2:c.8023A>G
ENST00000528762.2:c.8023A>G
ENST00000530893.7:c.7654A>G
ENST00000665585.2:c.8023A>G
ENST00000666593.2:c.8023A>G
ENST00000700202.2:c.8023A>G
ENST00000700202.1:c.490A>G
ENST00000380152.8:c.8023A>G
ENST00000544455.6:c.8023A>G
ENST00000614259.2:c.8031A>G
ENST00000665585.1:c.588A>G
ENST00000680887.1:c.8023A>G
ENST00000380152.7:c.8023A>G
ENST00000544455.5:c.8023A>G
NM_000059.3:c.8023A>G
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Pathogenic

Met criteria codes 2
PP4_Strong PVS1
Not Met criteria codes 3
BS1 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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ENIGMA BRCA1 and BRCA2 VCEP
The c.8023A>G variant in BRCA2 is a missense variant predicted to cause substitution of Isoleucine by Valine at amino acid 2675 (p.Ile2675Val). 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 variant is reported to result in aberrant mRNA splicing. RT-PCR and mini-gene assays demonstrated that the variant impacts splicing by creation of a donor site, resulting in skipping of 309nt of exon 18 (PMIDs: 18424508, 22505045, 28339459). All studies report no wild-type transcript from the variant allele. Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1612 (based on Cosegregation LR=605.1; Pathology LR=0.88; Co-occurrence LR=1.05; Family History LR=2.88), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 31131967). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA2-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PVS1 (RNA), PP4_Very strong).
Met criteria codes
PP4_Strong
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 1612 (based on Cosegregation LR=605.1; Pathology LR=0.88; Co-occurrence LR=1.05; Family History LR=2.88), above the threshold for Very strong evidence towards pathogenicity (LR >350) (PP4_Very strong met; PMID: 31131976).
PVS1
This variant is reported to result in aberrant mRNA splicing. RT-PCR and mini-gene assays demonstrated that the variant impacts splicing by creation of a donor site, resulting in skipping of 309nt of exon 18 (PMIDs: 18424508, 22505045, 28339459). All studies report no wild-type transcript from the variant allele. Appropriate code strength determined by comparison of results to PVS1 decision tree (PVS1 (RNA) met).
Not Met criteria codes
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).
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).
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
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