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TP53
Final classification
VUS
PM2BP4
TP53
c.214C>T
p.Pro72Ser
This variant

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).

Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.214C>T
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 applied · 13 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is present at very low frequency in population databases. In gnomAD v2.1, the total allele frequency is 0.00160% (4/250,672 alleles), below the VCEP PM2_Supporting threshold of 0.003%. The highest subpopulation frequency (European non-Finnish) is 0.00353% (4/113,442 alleles), below the VCEP subpopulation cutoff of 0.004%. In gnomAD v4.1, the total allele frequency is 0.00068% (11/1,613,668 alleles). The variant is absent from gnomAD-Canada v1.0.
gnomAD v2.1 total AF=0.00160% (<0.003% PM2_Supporting threshold)gnomAD v2.1 grpmax FAF=1.12e-05 (NFE subpopulation AF=0.00353% < 0.004%)gnomAD v4.1 total AF=0.00068%
BP4 moderate Benign
The TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2) directly assigns BP4_moderate to c.214C>T (p.Pro72Ser). The variant has a BayesDel score of -0.202922 (Class C0), which is ≤ -0.008, meeting the VCEP BP4_Moderate threshold. aGVGD class is C0 (not C65, so no exclusion applies). SpliceAI predicts no splicing impact (max delta = 0.00, which is < 0.2), satisfying the requirement of no predicted splicing differences.
VCEP PP3-BP4-codes.xlsx directly assigns BP4_moderate to c.214C>TBayesDel -0.202922 ≤ -0.008 (meets BP4_Moderate threshold)aGVGD Class C0 (not C65
Assessed · not applied · 10 not met · 3 not assessed
Pathogenic
PS2 No de novo observation data are available for this variant.
PS3 The TP53 VCEP Functional-worksheet (Supplementary Table S3) does not contain an entry for the p.Pro72Ser (P72S) amino acid substitution.
PS4 No proband-level phenotype data or LFS cancer point tallies are available in the case materials.
PM1 Codon 72 is not among the TP53 VCEP-defined mutational hotspots (codons 175, 245, 248, 249, 273, 282).
PM5 Codon 72 is a known common polymorphic site (rs1042522, Pro72Arg).
PP1 No cosegregation data are available for this variant.
PP3 The TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2) directly assigns BP4_moderate to c.214C>T, not PP3.
PP4 PP4 under the TP53 VCEP is based on variant allele fraction (VAF) observations in blood specimens (5-25% for Moderate, 5-35% for Supporting), reflecting concern for clonal hematopoiesis/somatic mosaicism.
Benign
BA1 The highest filtering allele frequency (FAF) observed in any gnomAD continental subpopulation is 1.12e-05 (gnomAD v2.1, European non-Finnish).
BS1 The highest filtering allele frequency in any gnomAD continental subpopulation is 1.12e-05 (v2.1 grpmax FAF), which falls below the VCEP BS1 threshold of ≥ 0.0003 (0.03%).
BS2 No data are available regarding observation of this variant in unrelated females who have reached at least 60 years of age without cancer, as required for BS2 under the TP53 VCEP.
BS3 The TP53 VCEP Functional-worksheet (Supplementary Table S3) does not contain an entry for the p.Pro72Ser (P72S) amino acid substitution.
BS4 No segregation data are available to assess lack of segregation with LFS-associated cancers in affected family members, as required for BS4 under the TP53 VCEP.
N/A · 10 PVS1 · PS1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP5 · BP6 · BP7
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