Starting
Initialising…
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RAD51D
Final classification
VUS
RAD51D c.446T>A · p.Leu149Gln
RAD51D

NM_002878.4:c.446T>A (p.Leu149Gln) is a missense variant in exon 5 of RAD51D, a moderate-penetrance breast and ovarian cancer susceptibility gene.

Gene
RAD51D
Transcript
NM_002878.4
HGVS · transcript:coding
NM_002878.4:c.446T>A
Consequence
N/A
GRCh38
chr17:35107022 A>T
GRCh37
chr17:33434041 A>T
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: none; combination = no applied criteria, 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: none; combination = no applied criteria, which maps to VUS.
Classification rationale
VUS
RAD51D c.446T>A

NM_002878.4:c.446T>A (p.Leu149Gln) is a missense variant in exon 5 of RAD51D, a moderate-penetrance breast and ovarian cancer susceptibility gene. Population frequency data from gnomAD v2.1 and v4.1 are unavailable; gnomAD-Canada reports zero observations. The variant cannot be confirmed as absent or rare in population controls.1 In silico predictions are inconclusive: REVEL (0.434) is intermediate, BayesDel (0.295) is borderline, and SpliceAI predicts no splicing impact (max delta 0.03). Neither PP3 nor BP4 criteria are met.2 The variant is reported in ClinVar as Uncertain significance by a single clinical laboratory (Labcorp Genetics/Invitae, SCV007364796) with criteria provided.3 No functional studies, de novo reports, segregation data, case-control studies, or same-residue pathogenic comparators were identified for this variant. No pathogenic or benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines.4

2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002878.4 · variants mapped to exon structure
RAD51D NM_002878.4
Fetching transcript structure from UCSC…
Applied criteria · 0 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
      Population frequency
      This variant is absent from gnomAD v4.1.
      This variant is absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 4705017)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.434. BayesDel score = 0.294753.
      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.
      Literature · 1 PMIDs triaged
      1papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots