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RAD51C
Final classification
VUS
RAD51C c.431T>C · p.Ile144Thr
RAD51C

NM_058216.3:c.431T>C (p.Ile144Thr) in RAD51C is a rare missense variant with extremely low population frequency (gnomAD v2.1 AF=0.0057%, v4.1 AF=0.014%). The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel has published RAD51C specifications (version 1.0.0) but no per-criterion rules were available for direct application; generic ACMG/AMP 2015 criteria were used as fallback.

Gene
RAD51C
Transcript
NM_058216.3
HGVS · transcript:coding
NM_058216.3:c.431T>C
Consequence
N/A
GRCh38
chr17:58696719 T>C
GRCh37
chr17:56774080 T>C
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, BP6 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, BP6 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP6 VUS
RAD51C c.431T>C

NM_058216.3:c.431T>C (p.Ile144Thr) in RAD51C is a rare missense variant with extremely low population frequency (gnomAD v2.1 AF=0.0057%, v4.1 AF=0.014%). The ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel has published RAD51C specifications (version 1.0.0) but no per-criterion rules were available for direct application; generic ACMG/AMP 2015 criteria were used as fallback.1 The variant is absent or at extremely low frequency in population databases, meeting PM2 at supporting strength (gnomAD v4.1 overall AF=0.014%; 0 homozygotes). gnomAD v4.1 Middle Eastern subpopulation AF=0.279% is noted but remains below the BS1 threshold of 0.3%.2 Myriad Genetics classified this variant as Likely benign (SCV004019909, criteria provided), meeting BP6 at supporting strength. However, the cited reference (PMID:25085752) is a BRCA1/BRCA2 reclassification algorithm and does not provide RAD51C-specific evidence.3 In silico predictions are inconclusive: REVEL 0.314, BayesDel 0.041, SpliceAI delta 0.01, with Polyphen-2/SIFT suggesting possible damage but SNPs&GO predicting neutrality (PMID:23117857). Neither PP3 nor BP4 is met.4 The variant has been observed in one Iraqi Jewish breast cancer proband (PMID:23117857) and one Danish HBOC family (PMID:26740214) but at insufficient frequency for PS4. No functional studies (PS3/BS3), segregation data (PP1/BS4), or de novo observations (PS2/PM6) are available.5 The variant is not located in a statistically significant hotspot (PM1 not met), no alternative nucleotide changes at the same residue are established as pathogenic (PM5 not applicable), and RAD51C is not a gene with a low rate of benign missense variation (PP2 not met).6 Overall classification: Uncertain significance. One supporting pathogenic criterion (PM2) is balanced by one supporting benign criterion (BP6), with all other criteria either not met or not applicable. This results in indeterminate classification under ACMG/AMP 2015 combination rules.7

PM2 + BP6 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= 0.000141875; MAF= 0.01419%, 229/1614096 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.00279421; MAF= 0.27942%, 17/6084 alleles, homozygotes = 0); grpmax FAF= 0.0017798.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 5.65615e-05; MAF= 0.00566%, 16/282878 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000240308; MAF= 0.02403%, 6/24968 alleles, homozygotes = 0); grpmax FAF= 0.00015629.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.014% · 229 / 1,614,096
      0 hom · FAF 0.18%
      Middle Eastern
      17 / 6,084
      0.28%
      African/African American
      15 / 74,944
      0.02%
      European (non-Finnish)
      186 / 1,180,046
      0.016%
      Remaining individuals
      7 / 62,484
      0.011%
      Admixed American
      3 / 60,004
      0.005%
      South Asian
      1 / 91,090
      0.0011%
      + 4 not observed (European (Finnish), Amish, East Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0057% · 16 / 282,878
      0 hom · FAF 0.016%
      African/African American
      6 / 24,968
      0.024%
      European (non-Finnish)
      10 / 129,184
      0.0077%
      + 6 not observed (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 (18 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 142840)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.314. BayesDel score = 0.0405109.
      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 · 8 PMIDs not cited in assessment
      23117857 ↗ Germline mutations in RAD51C in Jewish high cancer risk families. 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
      26261251 ↗ Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population. CLINVAR
      26740214 ↗ Identification of six pathogenic RAD51C mutations via mutational screening of 1228 Danish individuals with increased risk of hereditary breast and/or ovarian cancer. CLINVAR
      36099300 ↗ Homologous recombination-deficient mutation cluster in tumor suppressor RAD51C identified by comprehensive analysis of cancer variants. CLINVAR
      21537932 ↗ A HRM-based screening method detects RAD51C germ-line deleterious mutations in Spanish breast and ovarian cancer families. CLINVAR
      22538716 ↗ Germline RAD51C mutations confer susceptibility to ovarian cancer. CLINVAR
      25186627 ↗ Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel. CLINVAR