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TP53
Final classification
VUS
TP53 c.214_215delinsTG · p.Pro72Cys
TP53

NM_000546.5:c.214_215delinsTG (p.Pro72Cys) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting per TP53 VCEP criteria (allele frequency <0.003%).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.214_215delinsTG
Consequence
N/A
GRCh38
chr17:7676154 GG>CA
GRCh37
chr17:7579472 GG>CA
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
TP53 c.214_215delinsTG

NM_000546.5:c.214_215delinsTG (p.Pro72Cys) is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting per TP53 VCEP criteria (allele frequency <0.003%).1 PVS1 is not applicable as the variant is an in-frame delins resulting in a single amino acid substitution (p.Pro72Cys), not a null variant covered by the VCEP PVS1 flowchart.2 No functional data (PS3/BS3) is available for this variant; p.Pro72Cys is not listed in the VCEP Functional-worksheet and no variant-specific functional studies were identified in the reviewed literature.3 No pathogenic or likely pathogenic variant has been established at codon 72 (Pro72), which precludes application of PS1 and PM5. All single-nucleotide missense variants at this residue receive BP4_moderate per the VCEP.4 In silico scores (REVEL, BayesDel) are not computable for delins variants, precluding PP3/BP4 assessment.5 Codon 72 is not a recognized TP53 hotspot; the variant lies outside VCEP-designated hotspot codons 175, 245, 248, 249, 273, and 282, and is not listed in cancerhotspots.org.6 No proband clinical data, de novo observations, segregation data, or elderly cancer-free carrier data are available for this variant, precluding PS2, PS4, PP1, PP4, BS2, and BS4. This variant has been reported in ClinVar as Uncertain Significance, with 7 clinical laboratories reporting Uncertain Significance, 1 reporting Likely Benign, and the ClinGen TP53 VCEP Expert Panel classifying as Uncertain Significance (ClinVar ID: 182953).7 Applying the TP53 VCEP Tavtigian point-based classification system: only PM2_Supporting (1 point) is met, yielding a total of 1 point, which falls within the Uncertain Significance range (-1 to 5 points).8

PM2 VUS
2 cspec ↗pvs1_variant_assessment
3 vcep_functional_worksheet
4 vcep_pp3_bp4_codespm5_candidates
5 vcep_pp3_bp4_codes
8 cspec ↗final_classification_framework
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
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
      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 has been reported in ClinVar as Uncertain significance (7 clinical laboratories) and as Likely benign (1 clinical laboratory) and as Uncertain Significance by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 182953)
      SpliceAI screenshot
      In silico No data
      No in-silico prediction was recorded for this variant.
      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. TP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene 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 previously been reported in somatic cancers (COSMIC; COSV105026609, n = 2 times).
      Hotspots
      This variant does not lie 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 · 8 PMIDs not cited in assessment
      16818505 ↗ Functional analysis and molecular modeling show a preserved wild-type activity of p53(C238Y). CLINVAR
      17606709 ↗ Transcriptional functionality of germ line p53 mutants influences cancer phenotype. CLINVAR
      20407015 ↗ Altered-function p53 missense mutations identified in breast cancers can have subtle effects on transactivation. CLINVAR
      21343334 ↗ Dominant-negative features of mutant TP53 in germline carriers have limited impact on cancer outcomes. CLINVAR
      21519010 ↗ TP53 mutations in low-risk myelodysplastic syndromes with del(5q) predict disease progression. CLINVAR
      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
      26230955 ↗ TP53 mutations in de novo acute myeloid leukemia patients: longitudinal follow-ups show the mutation is stable during disease evolution. CLINVAR
      27276561 ↗ Genomic Classification and Prognosis in Acute Myeloid Leukemia. CLINVAR