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_007294.4(BRCA1):c.5509T>G (p.Trp1837Gly)

CA003681

55607 (ClinVar)

Gene: BRCA1
Condition: BRCA1-related cancer predisposition
Inheritance Mode: Autosomal dominant inheritance
UUID: 03c35580-6129-4df7-b7b4-8055d39efda1
Approved on: 2024-06-12
Published on: 2024-06-12

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
ENST00000461574.2:c.5506T>G
ENST00000470026.6:c.5509T>G
ENST00000473961.6:c.5383T>G
ENST00000476777.6:c.5503T>G
ENST00000477152.6:c.5431T>G
ENST00000478531.6:c.2197T>G
ENST00000489037.2:c.5431T>G
ENST00000493919.6:c.2059T>G
ENST00000494123.6:c.5509T>G
ENST00000497488.2:c.4621T>G
ENST00000618469.2:c.5509T>G
ENST00000634433.2:c.5386T>G
ENST00000644379.2:c.5575T>G
ENST00000644555.2:c.2059T>G
ENST00000652672.2:c.5368T>G
ENST00000484087.6:c.2071T>G
ENST00000700081.1:n.1392T>G
ENST00000700082.1:n.873T>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
More

Pathogenic

Met criteria codes 3
PP3 PM2_Supporting PP4_Strong
Not Met criteria codes 2
BS3 PS3

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 BRCA1 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.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
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).
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).
Curation History
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