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BRCA1
Final classification
Unclassified
BRCA1 c.1233T>G · p.Asp411Glu
BRCA1

NM_007294.3:c.1233T>G (p.Asp411Glu) is a missense variant in BRCA1 exon 10, classified as Benign by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel (ClinVar Variation ID: 41804).

Gene
BRCA1
Transcript
NM_007294.3
HGVS · transcript:coding
NM_007294.3:c.1233T>G
Consequence
N/A
GRCh38
chr17:43094298 A>C
GRCh37
chr17:41246315 A>C
Classification rationale
BS1BS3BP1BP6 Unclassified
BRCA1 c.1233T>G

NM_007294.3:c.1233T>G (p.Asp411Glu) is a missense variant in BRCA1 exon 10, classified as Benign by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel (ClinVar Variation ID: 41804).1 This variant is present in gnomAD v2.1 at 12/282,222 alleles (AF=4.25e-05) with a grpmax filter allele frequency of 0.024% (0.00024454) in the African/African American subpopulation (11/24,934 alleles), exceeding the ENIGMA BS1_Strong threshold of >0.01%.2 ENIGMA Table 9 (v1.2.0) assigns BS3_Strong to this variant based on calibrated functional assay evidence from Bouwman et al. 2020 (PMID:32546644), demonstrating protein function in homologous recombination repair complementation similar to benign control variants.3 Codon 411 is located outside all three (potentially) clinically important functional domains defined by ENIGMA for BRCA1: RING finger (aa 2-101), coiled-coil (aa 1391-1424), and BRCT repeats (aa 1650-1857). SpliceAI predicts no splicing impact (max delta score 0.07). These findings satisfy ENIGMA BP1_Strong criteria.4 Parsons et al. 2019 multifactorial likelihood analysis (PMID:31131967) reports a combined LR of 1.29, a segregation LR of 1.93, and a family history LR of 6.48 for this variant. The combined LR is in the neutral range and does not independently support either pathogenic (PP4) or benign (BP5) classification.5 No evidence was found to support any pathogenic criterion. PVS1, PS1, PS2, PS3, PS4, PS5, PM1, PM2, PM5, PM6, PP1, PP2, PP3, PP4, and PP5 are all either not met or not applicable.6 Under the ENIGMA Table 3 combination rules, two or more Strong Benign criteria support a Benign classification. The three Strong Benign criteria met (BS1_Strong, BS3_Strong, BP1_Strong) satisfy the Benign classification threshold.7

BS1 + BS3 + BP1 + BP6 Unclassified
3 vcep_specifications_table9_v1_2_2024_11_18
5 vcep_humu_40_1557_s001
Gene diagram · NM_007294.3 · variants mapped to exon structure
BRCA1 NM_007294.3
Fetching transcript structure from UCSC…
Applied criteria · 4 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.25197e-05; MAF= 0.00425%, 12/282222 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000441165; MAF= 0.04412%, 11/24934 alleles, homozygotes = 0); grpmax FAF= 0.00024454.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      0.0043% · 12 / 282,222
      0 hom · FAF 0.024%
      African/African American
      11 / 24,934
      0.044%
      Admixed American
      1 / 35,410
      0.0028%
      + 6 not observed (Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (5 clinical laboratories) and as Benign (4 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Benign by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 41804)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.639. BayesDel score = -0.196447.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 9 further PMIDs triaged but not cited — see Sources & References.
      Functional Categorization of BRCA1 Variants of Uncertain Clinical Significance in Homologous Recombination Repair Complementation Assays.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      BS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      15235020 ↗ Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation. CLINVAR
      15385441 ↗ Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. CLINVAR
      16267036 ↗ Application of embryonic lethal or other obvious phenotypes to characterize the clinical significance of genetic variants found in trans with known deleterious mutations. CLINVAR
      16518693 ↗ Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. CLINVAR
      21523855 ↗ Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      28283652 ↗ BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR