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TP53
Final classification
VUS
TP53 c.214C>T · p.Pro72Ser
TP53

NM_000546.5:c.214C>T (p.Pro72Ser) is a missense variant in exon 4 of TP53 at codon 72, a known common polymorphic site (rs1042522).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.214C>T
Consequence
N/A
GRCh38
chr17:7676155 G>A
GRCh37
chr17:7579473 G>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + BP4 moderate (-2) = -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) + BP4 moderate (-2) = -1 points, which maps to VUS.
Classification rationale
PM2 BP4 VUS
TP53 c.214C>T

NM_000546.5:c.214C>T (p.Pro72Ser) is a missense variant in exon 4 of TP53 at codon 72, a known common polymorphic site (rs1042522). The variant is present at very low frequency in gnomAD v2.1 (4/250,672 alleles; AF=0.00160%) and v4.1 (11/1,613,668 alleles; AF=0.00068%), meeting the TP53 VCEP PM2_Supporting threshold of <0.003% total allele frequency with subpopulation AF <0.004%.1 The variant is assigned BP4_moderate by the TP53 VCEP bioinformatic codes (Supplementary Table S2), with a BayesDel score of -0.202922 and no predicted splicing impact (SpliceAI max delta = 0.00).2 The variant has been reported in ClinVar as Likely benign (Ambry Genetics, 1 submission) and Uncertain significance (Labcorp/Invitae, 1 submission). No expert panel review is available. (ClinVar VariationID: 485023)3 The variant has been observed in somatic cancers (COSMIC, COSV52665238, n=6), but lies outside the TP53 VCEP-defined mutational hotspots (codons 175, 245, 248, 249, 273, 282). No functional data from VCEP-eligible assays are available for p.Pro72Ser; the variant is absent from the VCEP Functional-worksheet (Supplementary Table S3). Under the Tavtigian point-based system (TP53 VCEP v2.4.0), the evidence tally is PM2_Supporting (+1) + BP4_Moderate (-2) = -1 point, consistent with a classification of Uncertain Significance. The VCEP CAVEAT allowing reclassification of -1 points to Likely Benign (requiring ≥2 benign codes and PM2_Supporting as the only pathogenic code) is not met, as only one benign code (BP4_Moderate) is applied.

PM2 + BP4 VUS
2 vcep_pp3_bp4_codesbayesdelspliceai ↗
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
      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= 6.81677e-06; MAF= 0.00068%, 11/1613668 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33533e-05; MAF= 0.00134%, 1/74888 alleles, homozygotes = 0); grpmax FAF= 4.29e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.59571e-05; MAF= 0.00160%, 4/250672 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.52603e-05; MAF= 0.00353%, 4/113442 alleles, homozygotes = 0); grpmax FAF= 1.124e-05.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00068% · 11 / 1,613,668
      0 hom · FAF 0.00043%
      African/African American
      1 / 74,888
      0.0013%
      European (non-Finnish)
      10 / 1,179,974
      0.00085%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0016% · 4 / 250,672
      0 hom · FAF 0.0011%
      European (non-Finnish)
      4 / 113,442
      0.0035%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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 (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 485023)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.314. BayesDel score = -0.202922.
      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; COSV52665238, n = 6 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 · 5 PMIDs not cited in assessment
      20301488 ↗ Li-Fraumeni Syndrome. CLINVAR
      24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR