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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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_058216.3:c.30G>T 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. These frequencies are well below the 0.1% PM2 threshold for a rare disease variant.
gnomAD v2.1: 1/251450 (AF=0.0004%)gnomAD v4.1: 1/1
BP4 supporting Benign
Multiple in silico predictors suggest a benign effect. BayesDel score is -0.112 (negative, consistent with benign), REVEL score is 0.24 (below pathogenic threshold of 0.5), and SpliceAI max delta is 0.04 (no splicing impact). Three independent computational tools converge on a non-damaging prediction.
REVEL=0.24 (below pathogenic threshold)BayesDel=-0.112 (benign direction)SpliceAI max delta=0.04 (no splice impact)
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at codon 10 producing the same amino acid change (Met10Ile) has been established as pathogenic.
PS2 No de novo data available for this variant.
PS3 No variant-specific functional studies of NM_058216.3:c.30G>T (p.Met10Ile) were identified.
PS4 No variant-specific case-control association data available.
PM1 Met10 lies in the N-terminal region of RAD51C (residue 1–83), which is structurally flexible and not part of any known critical functional domain.
PM6 No de novo data available.
PP1 No co-segregation data available.
PP2 PP2 applies to genes with a low rate of benign missense variation where missense is a common disease mechanism.
PP3 In silico predictors do not support a damaging effect.
PP4 No patient-specific phenotype or family history data are available for this variant.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 The variant has an allele frequency far below the BA1 threshold (>1%).
BS1 The variant frequency is far below the BS1 threshold (>0.3% for non-VCEP).
BS2 No observation of this variant in a homozygous state or in trans with a pathogenic variant in a healthy adult.
BS3 No variant-specific functional studies demonstrating no damaging effect were identified.
BS4 No segregation data are available.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 No observation of this variant in trans with a known pathogenic variant in a healthy individual has been reported.
BP5 No data available on whether this variant has been observed in a case with an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 3 PVS1 · PM5 · BP7
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