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RAD51C
Final classification
VUS
RAD51C c.30G>T · p.Met10Ile
RAD51C

NM_058216.3:c.30G>T (p.Met10Ile) is a missense variant in exon 1 of RAD51C, a gene associated with autosomal dominant hereditary breast and ovarian cancer and autosomal recessive Fanconi anemia.

Gene
RAD51C
Transcript
NM_058216.3
HGVS · transcript:coding
NM_058216.3:c.30G>T
Consequence
N/A
GRCh38
chr17:58692673 G>T
GRCh37
chr17:56770034 G>T
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 benign; 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 benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
RAD51C c.30G>T

NM_058216.3:c.30G>T (p.Met10Ile) is a missense variant in exon 1 of RAD51C, a gene associated with autosomal dominant hereditary breast and ovarian cancer and autosomal recessive Fanconi anemia.1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 (1/251,450 alleles, AF=3.98e-6), gnomAD v4.1 (1/1,614,238 alleles, AF=6.19e-7), and absent from gnomAD-Canada, meeting PM2 at supporting level.2 Multiple in silico predictors suggest a benign effect: REVEL score is 0.24 (below the typical pathogenic threshold of 0.5), BayesDel score is -0.112 (consistent with benign), and SpliceAI predicts no splicing impact (max delta=0.04). This meets BP4 at supporting benign level.3 This variant has been reported in ClinVar as Uncertain significance by three clinical laboratories (ClinVar Variation ID: 538784). No expert panel has classified this variant as pathogenic or benign.4 The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel has published a specification document for RAD51C (Version 1.0.0), but the criterion-level rules are not yet structured for automated application. The generic ACMG/AMP 2015 framework was used as fallback.5 No variant-specific functional studies, segregation data, de novo reports, or case-control analyses were identified for this exact variant. The comprehensive RAD51C functional screen by Hu et al. 2023 (PMID:37253112) tested 173 missense variants but did not include p.Met10Ile.6 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is indeterminate. This variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 combination rules.7

PM2 + BP4 VUS
3 revelbayesdelspliceai ↗
5 cspec ↗generic_acmg_combination_rules
7 generic_acmg_combination_rules
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= 6.19487e-07; MAF= 0.00006%, 1/1614238 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47427e-07; MAF= 0.00008%, 1/1180042 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.97693e-06; MAF= 0.00040%, 1/251450 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.79214e-06; MAF= 0.00088%, 1/113738 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,238
      0 hom
      European (non-Finnish)
      1 / 1,180,042
      8.5e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0004% · 1 / 251,450
      0 hom
      European (non-Finnish)
      1 / 113,738
      0.00088%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (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 (3 clinical laboratories). (ClinVarID = 538784)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.24. BayesDel score = -0.112409.
      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 · 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
      34326862 ↗ Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. CLINVAR
      34923718 ↗ A decade of RAD51C and RAD51D germline variants in cancer. CLINVAR
      37253112 ↗ Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. CLINVAR
      20301575 ↗ Fanconi Anemia. 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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR