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TP53
Final classification
VUS
TP53 c.845G>T · p.Arg282Leu
TP53

NM_000546.5:c.845G>T (p.Arg282Leu) is a missense variant in exon 8 of TP53, assessed under the ClinGen TP53 Variant Curation Expert Panel specifications version 2.4.0 (Tavtigian point-based framework).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.845G>T
Consequence
N/A
GRCh38
chr17:7673775 C>A
GRCh37
chr17:7577093 C>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 moderate (+2) + BS3 strong (-4) = 1 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 moderate (+2) + BS3 strong (-4) = 1 points, which maps to VUS.
Classification rationale
PM1PM2PP3 BS3 VUS
TP53 c.845G>T

NM_000546.5:c.845G>T (p.Arg282Leu) is a missense variant in exon 8 of TP53, assessed under the ClinGen TP53 Variant Curation Expert Panel specifications version 2.4.0 (Tavtigian point-based framework).1 This variant affects codon 282, a well-established mutational hotspot within the DNA-binding domain explicitly listed in the TP53 VCEP PM1 rule. The residue is a statistically significant cancer hotspot with 10 somatic occurrences in COSMIC, satisfying PM1 at moderate strength (+2 points).2 The variant is extremely rare in population databases: gnomAD v4.1 reports an allele frequency of 3.10×10⁻⁶ (5/1,613,954 alleles; grpmax FAF=7.9×10⁻⁷), and it is absent from gnomAD v2.1. All subpopulation frequencies are well below the TP53 VCEP PM2_Supporting cutoff of <0.003%, satisfying PM2 at supporting level (+1 point).3 In silico predictors support a deleterious effect: aGVGD Class C65 with BayesDel score 0.360452 and REVEL score 0.898. Per the TP53 VCEP PP3-BP4-codes worksheet, this variant is assigned PP3_moderate (+2 points). SpliceAI predicts no splicing impact (max delta=0.00).4 Functional data from the TP53 VCEP Functional-worksheet demonstrates that p.Arg282Leu is functional in the Kato assay and shows no loss of function in Giacomelli, Kotler, and Kawaguchi assays. This satisfies BS3 at strong benign strength (−4 points): functional on Kato AND no LOF by the majority of eligible assays.5 The variant has been reported in ClinVar as Uncertain Significance by 6 clinical laboratories and as Uncertain Significance by the ClinGen TP53 Variant Curation Expert Panel (ClinVar ID: 182938). No proband data meeting Li-Fraumeni syndrome criteria was available for PS4 assessment.6 No de novo observations, cosegregation data, VAF data, or BS2/BS4 evidence was identified for this variant. PVS1 is not applicable to this missense variant. PS1 has no alternative nucleotide change comparator. PM5 requires curator review of VCEP classifications for comparator codon 282 variants. Final Tavtigian point total: PM1_Moderate (+2) + PM2_Supporting (+1) + PP3_Moderate (+2) + BS3_Strong (−4) = +1 point. This falls within the Uncertain Significance range (−1 to +5) per the TP53 VCEP v2.4.0 Tavtigian point-based rules. The classification is consistent with the ClinGen TP53 VCEP expert panel determination of Uncertain Significance for this variant.7

PM1 + PM2 + PP3 + BS3 VUS
4 vcep_pp3_bp4_codesbayesdelrevelspliceai ↗
5 vcep_functional_worksheetcspec ↗
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      This variant is present in gnomAD v4.1 (AF= 3.09798e-06; MAF= 0.00031%, 5/1613954 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.22926e-05; MAF= 0.00223%, 1/44858 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00031% · 5 / 1,613,954
      0 hom · FAF 7.9e-05%
      East Asian
      1 / 44,858
      0.0022%
      European (non-Finnish)
      4 / 1,180,030
      0.00034%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 (6 clinical laboratories) and as Uncertain Significance by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 182938)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.898. BayesDel score = 0.360452.
      Functional / OncoKB screenshot
      Functional Likely Neutral
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53068318, n = 10 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. ONCOKB
      29979965 ↗ A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. ONCOKB
      30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer. ONCOKB
      12365217 ↗ p53 mutations as tumor markers in fine needle aspirates of palpable breast masses. ONCOKB
      26619011 ↗ Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. ONCOKB
      27328919 ↗ TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data. ONCOKB
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR