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NM_002878.4:c.715C>T
p.Arg239Trp · RAD51D
ACMG/AMP
0%
complete
Final classification
Likely Benign
BP1BP4BP5
RAD51D
c.715C>T
p.Arg239Trp
missense · exon 8

RAD51D encodes a protein that works with other DNA-repair proteins to help accurately repair broken DNA through homologous recombination. Inherited changes in RAD51D increase the risk of ovarian cancer and may also increase breast cancer risk. RAD51D acts as a tumor-suppressor gene, and changes in it can contribute to chromosome instability and, rarely, resistance to chemotherapy in cancer cells.

This variant

This RAD51D variant occurs in a tumor-suppressor gene involved in homologous-recombination DNA repair, whose inherited loss-of-function changes increase ovarian cancer risk and may increase breast cancer risk.

Transcript
NM_002878.4
HGVS · transcript:coding
NM_002878.4:c.715C>T
GRCh38
chr17:35103277 G>A
GRCh37
chr17:33430296 G>A
Likely Benign: BP1, BP4, and BP5, each supporting, satisfy the generic ACMG/AMP fallback rule of at least two supporting benign criteria.
Classification rationale
BP1BP4BP5 Likely Benign
RAD51D c.715C>T missense · exon 8

BP1 supporting: RAD51D disease evidence is predominantly loss-of-function while the target is missense. BP4 supporting: the missense REVEL score of 0.287 meets the <=0.29 threshold. BP5 supporting: the variant repeatedly co-occurred with pathogenic RAD51D c.694C>T, providing an alternate molecular basis for reported disease.

BP1 + BP4 + BP5 → Likely Benign
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_002878.4 · variants mapped to exon structure
RAD51D NM_002878.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · 3
Strength Supporting Moderate Strong Very strong
BP1 supporting Benign
Met, supporting: RAD51D disease evidence is predominantly loss-of-function while the target is missense.
The gene-level disease context supports RAD51D loss of function as a germline disease mechanism.PMID:34923718 catalogs RAD51D missense variation but reports limited evidence for pathogenic missense disease mechanism, with only p.Ser207Leu reaching likely pathogenic classification in the review.The target variant is the missense change NM_002878.4:c.715C>T, p.Arg239Trp.
BP4 supporting Benign
Met at supporting strength: missense REVEL score 0.287 meets the <=0.29 BP4 supporting threshold.
The case identifies NM_002878.4:c.715C>T as the missense variant NP_002869.3:p.(Arg239Trp), requiring the REVEL path for PP3/BP4.REVEL score is 0.287, meeting the BP4 supporting threshold of <=0.29 from the ClinGen SVI REVEL calibration by Pejaver et al. 2022 (PMID:36413997).
BP5 supporting Benign
Met, supporting: c.715C>T repeatedly co-occurred with pathogenic RAD51D c.694C>T, providing an alternate molecular basis for the reported disease.
PMID:24130102 reports c.715C>T in six individuals, all of whom also carried pathogenic c.694C>T (p.Arg232*), and states the variants were probably in cis.PMID:22986143 reports p.R239W in a stage IV grade 3 ovarian-carcinoma subject who also carried a deleterious RAD51D mutation.Generic BP5 supporting evidence is a pathogenic variant found in a patient with a definitive alternate molecular basis for the phenotype; no RAD51D-specific VCEP rule was available.
Assessed · not applied · 11 not met · 9 not assessed
Pathogenic
PS1 Not assessed: no independent pathogenic p.Arg239Trp variant was documented in the reviewed evidence.
PS2 Not assessed: no documented parental testing proves de novo origin, and all six reported carriers also carried pathogenic c.694C>T in probable cis.
PS3 Not assessed: no validated variant-specific functional assay for RAD51D p.Arg239Trp was identified; available reports describe clinical observations or general RAD51D biology.
PS4 Not met: c.715C>T occurred in two ovarian-cancer patients but also four healthy carriers, without demonstrated variant-specific case-control enrichment.
PM1 Not met: p.Arg239Trp is not documented in an approved RAD51D critical domain or statistically significant hotspot.
PM2 Not met: ancestry-specific AF reaches 0.00084317 in gnomAD v4.1, exceeding the generic PM2 threshold of 0.0001 despite low overall AF.
PM5 Not assessed: no established pathogenic alternate missense variant at RAD51D residue Arg239 was documented.
PM6 Not assessed: the six reported carriers lacked documented parental-origin evidence and all also carried pathogenic c.694C>T, probably in cis.
PP1 Not assessed: six carriers were reported, but no informative meioses or phase-resolved segregation series isolate c.715C>T from pathogenic c.694C>T.
PP2 Not met: RAD51D disease evidence is predominantly loss-of-function, not an established missense mechanism.
PP3 Not met: missense REVEL score 0.287 is below the >=0.644 PP3 supporting threshold.
PP4 Not met: ovarian cancer is compatible with RAD51D disease but is not sufficiently specific, and c.715C>T was also found in four healthy carriers.
PP5 Not met: the exact variant has zero ClinVar expert-panel submissions, so no qualifying Pathogenic or Likely pathogenic classification exists.
Benign
BA1 Not met: gnomAD v4.1 maximum ancestry-specific AF is 0.00084317, far below the generic BA1 threshold of 0.05.
BS1 Not met: the highest observed gnomAD v4.1 ancestry-specific AF is 0.00084317, below the generic BS1 threshold of 0.01.
BS2 Not assessed: gnomAD v4.1 reports one homozygote, but age, health status, ascertainment, and phenotype are unavailable for BS2 interpretation.
BS3 Not assessed: no validated variant-specific normal-function assay for RAD51D p.Arg239Trp was identified; clinical observations and computational predictions cannot establish BS3.
BS4 Not assessed: four healthy carriers were reported, but age, pedigree, and phase-resolved data are insufficient to establish non-segregation of c.715C>T.
BP2 Not met: six reported carriers had pathogenic c.694C>T with c.715C>T, and the authors concluded the variants were probably in cis rather than trans.
BP6 Not met: two Likely benign ClinVar submissions are non-expert assertions, and the exact variant has zero expert-panel submissions.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency · supports benign
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= 1.98633e-05; MAF= 0.00199%, 32/1611014 alleles, homozygotes = 1) and has highest observed frequency in the Middle Eastern population (AF= 0.00084317; MAF= 0.08432%, 5/5930 alleles, homozygotes = 1); grpmax FAF= 0.0003318.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.25351e-05; MAF= 0.00325%, 9/276624 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000141323; MAF= 0.01413%, 1/7076 alleles, homozygotes = 0); grpmax FAF= 2.242e-05.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.002% · 32 / 1,611,014
1 hom · FAF 0.033%
Middle Eastern
5 / 5,930
0.084%
1 hom
African/African American
5 / 74,864
0.0067%
Remaining individuals
3 / 62,382
0.0048%
East Asian
1 / 44,828
0.0022%
Admixed American
1 / 59,542
0.0017%
European (non-Finnish)
16 / 1,178,930
0.0014%
South Asian
1 / 90,320
0.0011%
+ 3 not observed (European (Finnish), Amish, Ashkenazi Jewish)
gnomAD v2.1
0.0033% · 9 / 276,624
0 hom · FAF 0.0022%
Remaining individuals
1 / 7,076
0.014%
East Asian
2 / 19,676
0.01%
European (non-Finnish)
5 / 126,380
0.004%
South Asian
1 / 29,706
0.0034%
+ 4 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish))
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 (13 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 187225)
SpliceAI screenshot
In silico
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here. REVEL score = 0.287. BayesDel score = 0.0376745.
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 previously been reported in somatic cancers (COSMIC; COSV114987211, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
4papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & references.
Loss of function germline mutations in RAD51D in women with ovarian carcinoma.
Searched
c.715C>Tp.R239WNP_002869.3:p.(R239W)
Found
This study reports p.R239W among rare RAD51D missense variants in a stage IV ovarian-cancer subject; the subject also carried a deleterious RAD51D mutation, and the table reports no loss of heterozygosity, PolyPhen-2 0.999, and SIFT P=0.41.
Variant
✓ Names this variant — characterised directly
Applied to
→BP5 supporting
Reports p.R239W in a subject who also carried a deleterious RAD51D mutation.
In addition to the three subjects with RAD51D mutations, five subjects carried rare missense variants in RAD51D: p.C9S, p.S46C, p.S207L, p.R239W, and p.I311N (Table 2).
Location Results, paragraph 5; Table 2, CF 820.01  ·  Context Bidirectional Sanger sequencing of RAD51D exons and intron-exon boundaries in 360 ovarian/peritoneal/fallopian-tube carcinoma subjects and 459 familial breast-cancer patients.  ·  full text
About 1% of the breast and ovarian Spanish families testing negative for BRCA1 and BRCA2 are carriers of RAD51D pathogenic variants.
Searched
c.715C>TNP_002869.3:p.(R239W)p.Arg239Trp
Found
This study explicitly reports RAD51D c.715C>T (p.Arg239Trp) in six individuals, all also carrying the pathogenic c.694C>T (p.Arg232*) variant; the authors considered the variants probably in cis and reported damaging predictions from two of four in-silico tools.
Variant
✓ Names this variant — characterised directly
Applied to
→BP5 supporting
Reports recurrent co-occurrence with pathogenic RAD51D c.694C>T and probable cis phase.
Both the affected and healthy carriers (six subjects) also carried the missense change c.715C>T (p.Arg239Trp) in exon 8 (Table 1).
Location Results, paragraph describing carriers of c.694C>T; Table 1; Discussion  ·  Context Germline RAD51D screening in 842 Spanish index cases from breast and/or ovarian cancer families, using direct sequencing, high-resolution melting, and denaturing high-performance liquid chromatography; protein effects were assessed with four in-silico tools.  ·  full text
Rule & framework references · cited for criterion definitions, not variant evidence
34923718 ↗ A decade of RAD51C and RAD51D germline variants in cancer.
37344587 ↗ Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 4 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
26261251 ↗ Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population. CLINVAR
30306255 ↗ Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings. 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