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RAD50
Final classification
VUS
RAD50 c.2301dup · p.Ile768HisfsTer14
RAD50

NM_005732.3:c.2301dup (p.Ile768HisfsTer14) is a frameshift duplication in exon 14 of RAD50, predicted to undergo nonsense-mediated decay. RAD50 loss of function is an established disease mechanism for RAD50 deficiency syndrome.

Gene
RAD50
Transcript
NM_005732.3
HGVS · transcript:coding
NM_005732.3:c.2301dup
Consequence
N/A
GRCh38
chr5:132603392 A>AC
GRCh37
chr5:131939084 A>AC
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: PVS1 strong, PM2 supporting; combination = 1 strong + 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: PVS1 strong, PM2 supporting; combination = 1 strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
RAD50 c.2301dup

NM_005732.3:c.2301dup (p.Ile768HisfsTer14) is a frameshift duplication in exon 14 of RAD50, predicted to undergo nonsense-mediated decay. RAD50 loss of function is an established disease mechanism for RAD50 deficiency syndrome.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with a rare pathogenic variant.2 No variant-specific functional data, clinical case reports, de novo observations, or segregation data were identified in the reviewed literature. Four RAD50 gene-level publications were reviewed but none reported this specific variant. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), one strong criterion (PVS1) plus one supporting criterion (PM2) yields a classification of Likely Pathogenic.3

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
3 generic_acmg_combination_rules
Gene diagram · NM_005732.3 · variants mapped to exon structure
RAD50 NM_005732.3
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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 · 4 PMIDs not cited in assessment
      12208847 ↗ Cancer predisposition and hematopoietic failure in Rad50(S/S) mice. ONCOKB
      14684699 ↗ Mutation screening of Mre11 complex genes: indication of RAD50 involvement in breast and ovarian cancer susceptibility. ONCOKB
      16288216 ↗ Microsatellite instability and mutation analysis of candidate genes in urothelial cell carcinomas of upper urinary tract. ONCOKB
      21892167 ↗ The Rad50 coiled-coil domain is indispensable for Mre11 complex functions. ONCOKB