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RAD51D
Final classification
VUS
PM2
RAD51D
c.422T>C
p.Leu141Pro
This variant

NM_002878.3:c.422T>C (p.Leu141Pro) is a missense variant in RAD51D, a moderate-penetrance ovarian cancer predisposition gene where loss-of-function is the established disease mechanism.

Transcript
NM_002878.3
HGVS · transcript:coding
NM_002878.3:c.422T>C
GRCh38
chr17:35107046 A>G
GRCh37
chr17:33434065 A>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
RAD51D c.422T>C

NM_002878.3:c.422T>C (p.Leu141Pro) is a missense variant in RAD51D, a moderate-penetrance ovarian cancer predisposition gene where loss-of-function is the established disease mechanism.1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=0.0004% (1/251,470 alleles) and gnomAD v4.1 AF=0.0011% (18/1,614,128 alleles), and is absent from gnomAD-Canada. PM2 (supporting) is met.2 ClinVar reports this variant as Uncertain significance by seven clinical laboratories with review status 'criteria provided, single submitter.' No expert panel pathogenic or benign classification exists.3 In silico predictions are mixed: REVEL score 0.44 (indeterminate), BayesDel score 0.07 (benign), and SpliceAI max delta 0.04 (no splice impact). These do not meet PP3 or BP4 thresholds.4 No functional studies, case-control data, cosegregation data, or de novo observations are available for this variant. PS3, PS4, PP1, PS2, and PM6 remain unassessed. No same-residue pathogenic comparator exists at Leu141, precluding PS1 and PM5 application.5 RAD51D has both established pathogenic truncating and missense variants; BP1 is not met because missense variants cannot be presumed benign in this gene.6 Overall, this variant meets only PM2 (supporting). All other applicable criteria are either not met or cannot be assessed due to insufficient evidence. The variant remains of uncertain significance.

PM2 VUS
1 pvs1_gene_context
4 revelbayesdelspliceai ↗
5 pm5_candidates
6 pvs1_gene_context
Gene diagram · NM_002878.3 · variants mapped to exon structure
RAD51D NM_002878.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 20 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_002878.3:c.422T>C is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.98e-06 (1/251,470 alleles, 0.0004%) and gnomAD v4.1 AF=1.12e-05 (18/1,614,128 alleles, 0.0011%). Both are well below the 0.1% threshold for PM2. Absent from gnomAD-Canada v1.0.
gnomAD v2.1: 1/251470 alleles (AF=0.0004%)gnomAD v4.1: 18/1
Assessed · not applied · 9 not met · 11 not assessed
Pathogenic
PS1 No known pathogenic variant with a different amino acid change at the same residue (Leu141) was identified.
PS2 No de novo data available for NM_002878.3:c.422T>C.
PS3 No variant-specific functional studies identified.
PS4 No case-control or cohort studies comparing the prevalence of NM_002878.3:c.422T>C in affected vs.
PM1 Leu141 does not lie in a statistically significant mutational hotspot in RAD51D.
PM6 No de novo data available.
PP1 No cosegregation data available.
PP2 PP2 requires a gene where missense variants are a common mechanism of disease AND the gene has a low rate of benign missense variation.
PP3 In silico predictions are mixed and do not consistently support a deleterious effect.
PP4 No patient phenotype or family history data are available to assess whether the clinical presentation is highly specific for RAD51D-associated disease.
PP5 No reputable source has recently reported NM_002878.3:c.422T>C as pathogenic.
Benign
BA1 gnomAD v4.1 allele frequency is 0.0011% (1.12e-05), well below the 1% threshold for BA1.
BS1 gnomAD v4.1 allele frequency is 0.0011%, well below the 0.3% threshold for BS1.
BS2 No data on observation of this variant in healthy adults where full penetrance would be expected at an early age.
BS3 No functional studies have been performed on NM_002878.3:c.422T>C (p.Leu141Pro) that demonstrate no damaging effect on protein function or splicing.
BS4 No cosegregation data demonstrating lack of segregation with disease are available for this variant.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 No data on observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant.
BP4 Computational evidence does not consistently suggest no impact.
BP6 No reputable source has recently reported NM_002878.3:c.422T>C as benign.
N/A · 7 PVS1 · PM3 · PM4 · PM5 · BP3 · BP5 · 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= 1.11515e-05; MAF= 0.00112%, 18/1614128 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.5254e-05; MAF= 0.00153%, 18/1180018 alleles, homozygotes = 0); grpmax FAF= 9.53e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97662e-06; MAF= 0.00040%, 1/251470 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.79152e-06; MAF= 0.00088%, 1/113746 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0011% · 18 / 1,614,128
0 hom · FAF 0.00095%
European (non-Finnish)
18 / 1,180,018
0.0015%
+ 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 / 251,470
0 hom
European (non-Finnish)
1 / 113,746
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 (7 clinical laboratories). (ClinVarID = 186683)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.44. BayesDel score = 0.0702953.
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. RAD51D, a DNA repair protein, is infrequently altered in cancer.
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
8Sources
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
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