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TP53
Final classification
Likely Pathogenic
TP53 c.580del · p.Ile195SerfsTer52
TP53

NM_000546.5:c.580delC (p.Ile195SerfsTer52) is a frameshift deletion in exon 6 of TP53, producing a premature termination codon at position 246, upstream of p.Lys351, and is predicted to undergo nonsense-mediated decay. Under the TP53 VCEP PVS1 decision tree (v2.4.0), PVS1 is applied at very strong weight (8 points).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.580del
Consequence
N/A
GRCh38
chr17:7674950 AG>A
GRCh37
chr17:7578268 AG>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PVS1 very strong (+8) + PM2 supporting (+1) = 9 points, which maps to Likely Pathogenic.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PVS1 very strong (+8) + PM2 supporting (+1) = 9 points, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.580del

NM_000546.5:c.580delC (p.Ile195SerfsTer52) is a frameshift deletion in exon 6 of TP53, producing a premature termination codon at position 246, upstream of p.Lys351, and is predicted to undergo nonsense-mediated decay. Under the TP53 VCEP PVS1 decision tree (v2.4.0), PVS1 is applied at very strong weight (8 points).1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. Under the TP53 VCEP PM2 specifications, variants with an allele frequency below 0.00003 qualify for PM2 at supporting level (1 point).2 The variant is absent from ClinVar and has not been reported in COSMIC. No variant-specific functional data are available from the TP53 VCEP functional worksheet (which covers missense and in-frame deletions only). No proband phenotype, de novo, segregation, or VAF data are available in the case materials to assess PS2, PS4, PP1, PP4, BS2, or BS4.3 Total weighted points: PVS1 (8) + PM2_Supporting (1) = 9 points. Per the TP53 VCEP Tavtigian Bayesian point-based classification framework (v2.4.0), 6-9 points corresponds to Likely Pathogenic.4

PVS1 + PM2 Likely Pathogenic
1 cspec ↗vcep_pvs1_flowchartpvs1_variant_assessment
4 final_classification_framework
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
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 · supports pathogenic
      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 Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      11753428 ↗ A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer. ONCOKB
      11900253 ↗ Rescuing the function of mutant p53. ONCOKB
      16007150 ↗ The relationship among p53 oligomer formation, structure and transcriptional activity using a comprehensive missense mutation library. ONCOKB
      19336573 ↗ High incidence of protein-truncating TP53 mutations in BRCA1-related breast cancer. ONCOKB
      21467160 ↗ Prognostic significance of truncating TP53 mutations in head and neck squamous cell carcinoma. ONCOKB