The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_007294.4(BRCA1):c.3418A>G (p.Ser1140Gly)

CA002212

41817 (ClinVar)

Gene: BRCA1
Condition: breast-ovarian cancer, familial, susceptibility to, 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 911b8df3-87b8-4dad-b9b9-792bc57a5295

HGVS expressions

NM_007294.4:c.3418A>G
NM_007294.4(BRCA1):c.3418A>G (p.Ser1140Gly)
NC_000017.11:g.43092113T>C
CM000679.2:g.43092113T>C
NC_000017.10:g.41244130T>C
CM000679.1:g.41244130T>C
NC_000017.9:g.38497656T>C
NG_005905.2:g.125871A>G
ENST00000357654.9:c.3418A>G
ENST00000471181.7:c.3418A>G
ENST00000352993.7:c.671-1081A>G
ENST00000354071.7:c.3418A>G
ENST00000357654.7:c.3418A>G
ENST00000461221.5:c.*3201A>G
ENST00000468300.5:c.788-1081A>G
ENST00000471181.6:c.3418A>G
ENST00000478531.5:c.785-1081A>G
ENST00000484087.5:c.410-1081A>G
ENST00000487825.5:c.413-1081A>G
ENST00000491747.6:c.788-1081A>G
ENST00000493795.5:c.3277A>G
ENST00000493919.5:c.647-1081A>G
ENST00000586385.5:c.5-28162A>G
ENST00000591534.5:c.-43-17592A>G
ENST00000591849.5:c.-99+33158A>G
NM_007294.3:c.3418A>G
NM_007297.3:c.3277A>G
NM_007298.3:c.788-1081A>G
NM_007299.3:c.788-1081A>G
NM_007300.3:c.3418A>G
NR_027676.1:n.3554A>G
NM_007297.4:c.3277A>G
NM_007299.4:c.788-1081A>G
NM_007300.4:c.3418A>G
NR_027676.2:n.3595A>G

Benign

Met criteria codes 5
BA1 BP5_Strong BP1_Strong BS3 BS2

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.3418A>G variant in BRCA1 is a missense variant predicted to cause substitution of Serine by Glycine at amino acid 1140 (p.Ser1140Gly). The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.03171 in the African/African-American population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met). This missense variant is located outside of a key functional domain and was not predicted to alter mRNA splicing using the SpliceAI predictor (score 0.06, score threshold <0.1) (BP1_Strong met). Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 32546644) (BS3 met). This variant has been observed in more than 10 individuals with features considered inconsistent with an FA-associated phenotype, and (Likely) Pathogenic variant seen in trans or variant is homozygous (total score 4 points) (BS2 met; Invitae internal contributor). Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.00029 (based on Co-occurrence LR=0.00029), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 16014699). In summary, this variant meets the criteria to be classified as a Benign variant for BRCA1-related cancer predisposition based on the ACMG/AMP criteria applied as specified by the ENIGMA BRCA1/2 VCEP (BA1, BP1_Strong, BS3, BS2, BP5_Very strong).
Met criteria codes
BA1
The highest non-cancer, non-founder population filter allele frequency in gnomAD v2.1 (exomes only, non-cancer subset, read depth ≥20) or gnomAD v3.1 (non-cancer subset, read depth ≥20) is 0.03171 in the African/African-American population, which is above the ENIGMA BRCA1/2 VCEP threshold (>0.001) for BA1 (BA1 met).
BP5_Strong
Multifactorial likelihood ratio analysis using clinically calibrated data produced a combined LR for this variant of 0.00029 (based on Co-occurrence LR=0.00029), below the threshold for Very strong benign evidence (LR <0.00285) (BP5_Very strong met; PMID: 16014699).
BP1_Strong
This missense variant is located outside of a key functional domain and was not predicted to alter mRNA splicing using the SpliceAI predictor (score 0.06, score threshold <0.1) (BP1_Strong met).
BS3
Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID: 32546644) (BS3 met).
BS2
This variant has been observed in more than 10 individuals with features considered inconsistent with an FA-associated phenotype, and (Likely) Pathogenic variant seen in trans or variant is homozygous (total score 4 points) (BS2 met; Invitae internal contributor).
Approved on: 2023-10-10
Published on: 2023-10-10
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.