Starting
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TP53
Final classification
VUS
TP53 c.509C>T · p.Thr170Met
TP53

NM_000546.5:c.509C>T (p.Thr170Met) is a missense variant in exon 5 of TP53. This variant is present at very low frequency in gnomAD v4.1 (AF=1.55e-05, 25/1,614,086 alleles, 0 homozygotes), meeting PM2_Supporting per the TP53 VCEP specifications (total AF < 0.003%; no non-founder subpopulation with multiple alleles exceeds 0.004%).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.509C>T
Consequence
N/A
GRCh38
chr17:7675103 G>A
GRCh37
chr17:7578421 G>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + BS3 supporting (-1) = 0 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) + BS3 supporting (-1) = 0 points, which maps to VUS.
Classification rationale
PM2 BS3BP6 VUS
TP53 c.509C>T

NM_000546.5:c.509C>T (p.Thr170Met) is a missense variant in exon 5 of TP53. This variant is present at very low frequency in gnomAD v4.1 (AF=1.55e-05, 25/1,614,086 alleles, 0 homozygotes), meeting PM2_Supporting per the TP53 VCEP specifications (total AF < 0.003%; no non-founder subpopulation with multiple alleles exceeds 0.004%).1 Functional assay data from the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3) demonstrates that p.Thr170Met is partially functional in the Kato et al. yeast transactivation assay and shows no loss of function across all available eligible assays (Funk, Giacomelli, Kotler), meeting BS3_Supporting per the VCEP functional rules.2 In silico predictions were evaluated per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2), which assigns 'No evidence' for c.509C>T — neither PP3 nor BP4 is met. The variant has aGVGD Class C15 and BayesDel score 0.321305.3 The variant has been reported in ClinVar with an expert panel classification of Likely Benign by the ClinGen TP53 Variant Curation Expert Panel (ClinVar ID: 184014). It has been observed in COSMIC as a somatic variant (n=14) but does not lie in a statistically significant cancer hotspot.4 PVS1, PS1, PS2, PS4, PS5, PM1, PM5, PM6, PP1, PP2, PP4, PP5, BA1, BS1, BS2, BS4, BP1, BP2, BP4, BP5, BP6, and BP7 are either not met, not assessed due to lack of evidence, or not applicable per the TP53 VCEP specifications.5 Tavtigian point total: PM2_Supporting (+1) + BS3_Supporting (−1) = 0 points, corresponding to a final classification of Uncertain Significance (VUS) per the TP53 VCEP v2.4.0 point-based system (VUS range: −1 to 5).6

PM2 + BS3 + BP6 VUS
2 vcep_functional_worksheetcspec ↗
3 vcep_pp3_bp4_codesbayesdel
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 1.54886e-05; MAF= 0.00155%, 25/1614086 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.2933e-05; MAF= 0.00329%, 3/91094 alleles, homozygotes = 0); grpmax FAF= 8.78e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.59842e-05; MAF= 0.00460%, 13/282706 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 7.74905e-05; MAF= 0.00775%, 10/129048 alleles, homozygotes = 0); grpmax FAF= 4.74e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0015% · 25 / 1,614,086
      0 hom · FAF 0.00088%
      South Asian
      3 / 91,094
      0.0033%
      European (Finnish)
      2 / 64,030
      0.0031%
      African/African American
      2 / 74,924
      0.0027%
      Admixed American
      1 / 60,000
      0.0017%
      European (non-Finnish)
      17 / 1,180,056
      0.0014%
      + 5 not observed (Remaining individuals, Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0046% · 13 / 282,706
      0 hom · FAF 0.0047%
      European (non-Finnish)
      10 / 129,048
      0.0077%
      African/African American
      1 / 24,954
      0.004%
      South Asian
      1 / 30,616
      0.0033%
      Admixed American
      1 / 35,434
      0.0028%
      + 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (5 clinical laboratories) and as Uncertain significance (3 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 184014)
      SpliceAI screenshot
      In silico
      REVEL score = 0.868. BayesDel score = 0.321305.
      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 previously been reported in somatic cancers (COSMIC; COSV52701457, n = 14 times).
      Hotspots
      This variant does not lie 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 · 9 PMIDs not cited in assessment
      11900253 ↗ Rescuing the function of mutant p53. ONCOKB
      8023157 ↗ Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. ONCOKB
      12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. CLINVAR
      17311302 ↗ Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. CLINVAR
      22653678 ↗ Prevalence of germline TP53 mutations and history of Li-Fraumeni syndrome in families with childhood adrenocortical tumors, choroid plexus tumors, and rhabdomyosarcoma: a population-based survey. CLINVAR
      23200980 ↗ Mutant TP53 in duodenal samples of pancreatic juice from patients with pancreatic cancer or high-grade dysplasia. 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
      28861920 ↗ Higher-than-expected population prevalence of potentially pathogenic germline TP53 variants in individuals unselected for cancer history. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR