Variant: NM_007294.4(BRCA1):c.5509T>G (p.Trp1837Gly)

CA003681

55607 (ClinVar)

Gene: BRCA1

Condition: breast-ovarian cancer, familial, susceptibility to, 1

Inheritance Mode: Autosomal dominant inheritance

UUID: 03c35580-6129-4df7-b7b4-8055d39efda1

HGVS expressions

NM_007294.4:c.5509T>G
NM_007294.4(BRCA1):c.5509T>G (p.Trp1837Gly)
NC_000017.11:g.43045761A>C
CM000679.2:g.43045761A>C
NC_000017.10:g.41197778A>C
CM000679.1:g.41197778A>C
NC_000017.9:g.38451304A>C
NG_005905.2:g.172223T>G
ENST00000357654.9:c.5509T>G
ENST00000471181.7:c.5572T>G
ENST00000644379.1:c.1896T>G
ENST00000352993.7:c.2083T>G
ENST00000357654.7:c.5509T>G
ENST00000461221.5:c.*5292T>G
ENST00000468300.5:c.*23T>G
ENST00000471181.6:c.5572T>G
ENST00000491747.6:c.2197T>G
ENST00000493795.5:c.5368T>G
ENST00000586385.5:c.439T>G
ENST00000591534.5:c.982T>G
ENST00000591849.5:c.208T>G
NM_007294.3:c.5509T>G
NM_007297.3:c.5368T>G
NM_007298.3:c.2197T>G
NM_007299.3:c.*23T>G
NM_007300.3:c.5572T>G
NR_027676.1:n.5645T>G
NM_007297.4:c.5368T>G
NM_007299.4:c.*23T>G
NM_007300.4:c.5572T>G
NR_027676.2:n.5686T>G

Pathogenic

• Met criteria codes: PP3 PM2_Supporting PP4_Strong

• Not Met criteria codes: PS3 BS3

Expert Panel

ENIGMA BRCA1 and BRCA2 VCEP

Criteria Specification Information

Criteria Specification: ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRCA1 Version 1.0.0

Evidence submitted by expert panel

ENIGMA BRCA1 and BRCA2 VCEP

The c.5509T>G variant in BRCA1 is a missense variant predicted to cause substitution of Tryptophan by Glycine at amino acid 1837 (p.Trp1837Gly). 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 BRCA1 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.533, above the recommended threshold of 0.28 for prediction of impact on BRCA1 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 three calibrated studies with discordant results. Exhibits protein function similar to pathogenic control variants (PMIDs: 30209399, 30765603) and between what was observed for benign and pathogenic control variants (PMID: 30257991) (PS3 and BS3 not met). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 2004.67 (based on Co-occurrence LR=1.067; Family History LR=1878.3), above the threshold for very strong evidence towards pathogenicity (>350) (PP4_Very strong met; PMIDs: 17924331, 31853058). In summary, this variant meets the criteria to be classified as a Pathogenic variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (PM2_Supporting, PP3, PP4_Very strong).

Met criteria codes

• PP3: This BRCA1 missense variant is within a key functional domain and the computational predictor BayesDel (noAF) gives a score of 0.533, above the recommended threshold of 0.28 for prediction of impact on BRCA1 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).
• PM2_Supporting: 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).
• PP4_Strong: Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 2004.67 (based on Co-occurrence LR=1.067; Family History LR=1878.3), above the threshold for very strong evidence towards pathogenicity (>350) (PP4_Very strong met; PMIDs: 17924331, 31853058).

Not Met criteria codes

• PS3: Reported by three calibrated studies with discordant results. Exhibits protein function similar to pathogenic control variants (PMIDs: 30209399, 30765603) and between what was observed for benign and pathogenic control variants (PMID: 30257991) (PS3 and BS3 not met).
• BS3: Reported by three calibrated studies with discordant results. Exhibits protein function similar to pathogenic control variants (PMIDs: 30209399, 30765603) and between what was observed for benign and pathogenic control variants (PMID: 30257991) (PS3 and BS3 not met).

Approved on: 2023-10-10

Published on: 2023-10-10