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MDM2
Final classification
VUS
MDM2 c.500G>A · p.Arg167Lys
MDM2

NM_002392.5:c.500G>A (NP_002383.2:p.Arg167Lys) is a missense variant in MDM2 that is absent from all gnomAD population databases (v2.1, v4.1, and gnomAD-Canada), meeting PM2 at supporting level.

Gene
MDM2
Transcript
NM_002392.5
HGVS · transcript:coding
NM_002392.5:c.500G>A
Consequence
N/A
GRCh38
chr12:68824628 G>A
GRCh37
chr12:69218408 G>A
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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
MDM2 c.500G>A

NM_002392.5:c.500G>A (NP_002383.2:p.Arg167Lys) is a missense variant in MDM2 that is absent from all gnomAD population databases (v2.1, v4.1, and gnomAD-Canada), meeting PM2 at supporting level.1 Multiple in silico tools uniformly predict a tolerated or benign effect: REVEL score 0.144, BayesDel score -0.333371, and SpliceAI max delta 0.00, meeting BP4 at supporting benign level.2 The variant is absent from ClinVar, COSMIC, and the published literature. No functional studies, segregation data, de novo reports, or case-control data are available. No CSPEC/VCEP framework exists for MDM2.3 With PM2 (supporting pathogenic) and BP4 (supporting benign) as the only met criteria and all other criteria not assessed, the evidence is insufficient for classification. The variant is classified as a Variant of Uncertain Significance (VUS) per generic ACMG/AMP 2015 criteria.4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002392.5 · variants mapped to exon structure
MDM2 NM_002392.5
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). REVEL score = 0.144. BayesDel score = -0.333371.
      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. MDM2, a ubiquitin ligase and p53 inhibitor, is amplified in a diverse range of cancers including well-differentiated liposarcomas.
      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