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RAD51D
Final classification
VUS
RAD51D c.422T>C · p.Leu141Pro
RAD51D

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.

Gene
RAD51D
Transcript
NM_002878.3
HGVS · transcript:coding
NM_002878.3:c.422T>C
Consequence
N/A
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 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= 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