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BRCA2
Final classification
Likely Benign
BRCA2 c.8183T>C · p.Val2728Ala
BRCA2

NM_000059.4:c.8183T>C (p.Val2728Ala) is a missense variant in exon 18 of BRCA2, located within the DNA binding domain (aa 2481-3186).

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.8183T>C
Consequence
N/A
GRCh38
chr13:32363385 T>C
GRCh37
chr13:32937522 T>C
Basis ENIGMA BRCA1/BRCA2 v1.2.0 Table 3 classification framework was used as the primary authority. The variant has 1 met Strong Benign criterion (BS3_Strong: calibrated functional assay shows HDR activity similar to benign controls, PMID:33609447) and 1 met Supporting Benign criterion (BP4_Supporting: BayesDel no-AF=0.103 ≤0.18, SpliceAI max delta=0.01 ≤0.1, inside DNA binding domain). No pathogenic criteria are met. The combination of 1 Strong (Benign) + 1 Supporting (Benign) satisfies the ENIGMA Table 3 Likely Benign rule. No conflicting evidence to resolve via the point system.
ENIGMA BRCA1/BRCA2 v1.2.0 Table 3 classification framework was used as the primary authority. The variant has 1 met Strong Benign criterion (BS3_Strong: calibrated functional assay shows HDR activity similar to benign controls, PMID:33609447) and 1 met Supporting Benign criterion (BP4_Supporting: BayesDel no-AF=0.103 ≤0.18, SpliceAI max delta=0.01 ≤0.1, inside DNA binding domain). No pathogenic criteria are met. The combination of 1 Strong (Benign) + 1 Supporting (Benign) satisfies the ENIGMA Table 3 Likely Benign rule. No conflicting evidence to resolve via the point system.
Classification rationale
BS3BP4 Likely Benign
BRCA2 c.8183T>C

NM_000059.4:c.8183T>C (p.Val2728Ala) is a missense variant in exon 18 of BRCA2, located within the DNA binding domain (aa 2481-3186). This variant is present at extremely low frequency in population databases: gnomAD v2.1 (1/31,400 alleles, exclusively in genomes; exome not covered) and gnomAD v4.1 (4/1,614,072 alleles, grpmax FAF=1.746e-05). It is absent from gnomAD-Canada v1.0.1 In ClinVar (Variation ID 141399), this variant is classified as Uncertain Significance by seven clinical laboratories and Likely Benign by one laboratory (criteria provided, single submitter).2 ENIGMA Specifications Table 9 assigns BS3_Strong based on a calibrated functional study (Richardson et al. 2021, PMID:33609447) demonstrating that V2728A exhibits HDR activity similar to benign control variants.3 ENIGMA BP4_Supporting is met: the variant is inside the DNA binding domain with no predicted impact via protein change (BayesDel no-AF=0.103, ≤0.18) and no predicted splicing impact (SpliceAI max delta=0.01, ≤0.1).4 The clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058) is LR=1.24 based on 1 proband, falling in the neutral zone and providing no evidence for PP4 or BP5.5 No pathogenic comparator exists at residue Val2728 (c.8182G>A p.Val2728Ile is classified as benign by ENIGMA), so PS1 is not met. PVS1, PM5, and other null-variant criteria are not applicable to this missense substitution.6 Applying ENIGMA Table 3 combination rules: BS3_Strong (1 Strong Benign) + BP4_Supporting (1 Supporting Benign) meets the likely benign rule [1 Strong (Benign) + 1 Supporting (Benign)]. The total benign evidence is one Strong and one Supporting criterion with no pathogenic criteria met.7

BS3 + BP4 Likely Benign
3 vcep_specifications_table9_v1_2_2024_11_18PMID:33609447 ↗
5 vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗
6 vcep_humu_40_1557_s001pm5_candidates
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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 · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 2.4782e-06; MAF= 0.00025%, 4/1614072 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33874e-05; MAF= 0.00534%, 4/74924 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.18471e-05; MAF= 0.00318%, 1/31400 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000114811; MAF= 0.01148%, 1/8710 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00025% · 4 / 1,614,072
      0 hom · FAF 0.0017%
      African/African American
      4 / 74,924
      0.0053%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
      gnomAD v2.1
      0.0032% · 1 / 31,400
      0 hom
      African/African American
      1 / 8,710
      0.011%
      + 7 not observed (Admixed American, 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 Uncertain significance (7 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 141399)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.614. BayesDel score = 0.103001.
      Functional / OncoKB screenshot
      Functional Likely Neutral
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
      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 previously been reported in somatic cancers (COSMIC; COSV105932213, n = 1 times).
      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. 7 further PMIDs triaged but not cited — see Sources & References.
      Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance.
      Found
      ENIGMA Table 9 BS3_Strong assignment: 'Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID:33609447) (BS3 met).'
      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 · 7 PMIDs not cited in assessment
      35736817 ↗ Classification of BRCA2 Variants of Uncertain Significance (VUS) Using an ACMG/AMP Model Incorporating a Homology-Directed Repair (HDR) Functional Assay. ONCOKB
      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
      31415627 ↗ A research-based gene panel to investigate breast, ovarian and prostate cancer genetic risk. CLINVAR
      31853058 ↗ Classification of variants of uncertain significance in BRCA1 and BRCA2 using personal and family history of cancer from individuals in a large hereditary cancer multigene panel testing cohort. CLINVAR
      32377563 ↗ Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR