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RAD51C
Final classification
VUS
RAD51C c.493A>G · p.Met165Val
RAD51C

NM_058216.3:c.493A>G (p.Met165Val) in RAD51C is a missense variant in exon 3. The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel specification for RAD51C (version 1.0.0) does not provide criterion-level rules; assessment follows generic ACMG/AMP 2015 guidelines.

Gene
RAD51C
Transcript
NM_058216.3
HGVS · transcript:coding
NM_058216.3:c.493A>G
Consequence
N/A
GRCh38
chr17:58696781 A>G
GRCh37
chr17:56774142 A>G
Basis ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAD51C Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAD51C Version 1.0.0 v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
RAD51C c.493A>G

NM_058216.3:c.493A>G (p.Met165Val) in RAD51C is a missense variant in exon 3. The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel specification for RAD51C (version 1.0.0) does not provide criterion-level rules; assessment follows generic ACMG/AMP 2015 guidelines.1 This variant is absent from gnomAD v2.1 and gnomAD-Canada and is extremely rare in gnomAD v4.1 (overall allele frequency 0.00012%, 2/1,614,182 alleles), meeting PM2 at supporting strength.2 Multiple in silico tools predict a benign effect: REVEL score 0.046, BayesDel score -0.475, and SpliceAI max delta 0.00, meeting BP4 at supporting strength.3 ClinVar reports this variant as uncertain significance (3 clinical laboratories) and benign (1 clinical laboratory). No expert panel classification is available. No publication identified mentions this specific variant.4 No functional studies, segregation data, case-control analyses, or de novo observations were identified for this variant. The variant has not been characterized experimentally. With PM2 (supporting) and BP4 (supporting) as the only applicable criteria, the evidence is balanced but insufficient for a definitive classification; the variant remains a variant of uncertain significance.

PM2 + BP4 VUS
Gene diagram · NM_058216.3 · variants mapped to exon structure
RAD51C NM_058216.3
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
      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= 1.23902e-06; MAF= 0.00012%, 2/1614182 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 1.56162e-05; MAF= 0.00156%, 1/64036 alleles, homozygotes = 0).
      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
      0.00012% · 2 / 1,614,182
      0 hom
      European (Finnish)
      1 / 64,036
      0.0016%
      European (non-Finnish)
      1 / 1,180,030
      8.5e-05%
      + 8 not observed (Remaining individuals, Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 Uncertain significance (3 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 482171)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.046. BayesDel score = -0.475232.
      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. RAD51C, a DNA repair protein, is altered by mutation or deletion in certain breast cancers.
      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 · 6 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
      18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
      19305347 ↗ ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome. CLINVAR
      23188549 ↗ NSGC practice guideline: risk assessment and genetic counseling for hereditary breast and ovarian cancer. CLINVAR
      25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR