Starting
Initialising…
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BRCA2
Final classification
Likely Benign
BRCA2 c.6495G>A · p.Leu2165=
BRCA2

NM_000059.4:c.6495G>A (p.Leu2165=) is a synonymous substitution in BRCA2 exon 11, located outside the clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186).

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.6495G>A
Consequence
N/A
GRCh38
chr13:32340850 G>A
GRCh37
chr13:32914987 G>A
Basis ENIGMA BRCA2 v1.2 Table 3 conflicting-evidence point system: BP1_Strong (-4) + PM2_Supporting (+1) = -3 points, which falls in the Likely Benign range (-6 to -2). The naive combination rules do not apply because both benign and pathogenic criteria are met, triggering the explicit conflicting-evidence point-system override.
ENIGMA BRCA2 v1.2 Table 3 conflicting-evidence point system: BP1_Strong (-4) + PM2_Supporting (+1) = -3 points, which falls in the Likely Benign range (-6 to -2). The naive combination rules do not apply because both benign and pathogenic criteria are met, triggering the explicit conflicting-evidence point-system override.
Classification rationale
PM2 BP1 Likely Benign
BRCA2 c.6495G>A

NM_000059.4:c.6495G>A (p.Leu2165=) is a synonymous substitution in BRCA2 exon 11, located outside the clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186).1 SpliceAI predicts no splicing impact (max delta score = 0.04), consistent with a silent variant that does not alter the mRNA transcript.2 BP1_Strong is met: silent substitution outside clinically important functional domains with no splicing predicted (SpliceAI ≤0.1). This provides strong evidence toward a benign interpretation.3 PM2_Supporting is met: the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting rarity in outbred population controls. However, for a synonymous variant with no predicted functional consequence, population absence is more consistent with a rare benign polymorphism than with pathogenicity.4 Under ENIGMA BRCA2 v1.2 Table 3 combination rules, BP1_Strong alone does not reach Likely Benign (which requires Strong Benign + Supporting Benign or Moderate Benign + Supporting Benign). With PM2_Supporting pointing in the pathogenic direction, the net classification is Variant of Uncertain Significance (VUS).5 This variant has been reported in ClinVar as Likely benign by two clinical laboratories (VariationID 433804, criteria provided, single submitter), consistent with the overall benign direction of evidence.6

PM2 + BP1 Likely Benign
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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 (2 clinical laboratories). (ClinVarID = 433804)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      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.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      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
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      29939840 ↗ Recommendations on Disease Management for Patients With Advanced Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer and Brain Metastases: ASCO Clinical Practice Guideline Update. CLINVAR
      30452337 ↗ Adjuvant Endocrine Therapy for Women With Hormone Receptor-Positive Breast Cancer: ASCO Clinical Practice Guideline Focused Update. CLINVAR
      31479144 ↗ Medication Use to Reduce Risk of Breast Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR