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TP53
Final classification
VUS
TP53 c.293C>G · p.Pro98Arg
TP53

PM2_Supporting is met: NM_000546.6:c.293C>G (p.Pro98Arg) is absent from gnomAD v2.1 and v4.1 (0 alleles across all populations), satisfying the VCEP PM2_Supporting threshold of allele frequency <0.00003.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.293C>G
Consequence
N/A
GRCh38
chr17:7676076 G>C
GRCh37
chr17:7579394 G>C
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + PP3 moderate (+2) = 3 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) + PP3 moderate (+2) = 3 points, which maps to VUS.
Classification rationale
PM2PP3 VUS
TP53 c.293C>G

PM2_Supporting is met: NM_000546.6:c.293C>G (p.Pro98Arg) is absent from gnomAD v2.1 and v4.1 (0 alleles across all populations), satisfying the VCEP PM2_Supporting threshold of allele frequency <0.00003.1 PP3_Moderate is met: The VCEP PP3-BP4-codes.xlsx assigns PP3_moderate for c.293C>G. This variant has aGVGD Class C65 and BayesDel score 0.591769 (≥0.16), with no predicted splicing impact (SpliceAI max delta 0.00). REVEL score of 0.955 provides additional in silico support.2 PVS1 is not applicable: this is a missense variant; the TP53 VCEP reserves PVS1 for null variants (nonsense, frameshift, canonical splice, initiation codon, exon deletions).3 PS3 and BS3 are not met: the VCEP Functional-worksheet.xlsx assigns 'No evidence' for p.Pro98Arg. Kato class is 'Partially functional' and Giacomelli reports 'noLOF', which does not satisfy VCEP PS3 or BS3 criteria thresholds.4 PM1 is not met: codon 98 is not among the VCEP-defined hotspot codons (175, 245, 248, 249, 273, 282), and the residue is not a statistically significant hotspot on cancerhotspots.org. PM5 is not met: no other Pro98 missense variant has a VCEP P/LP classification.5 PS1, PS2, PS4, PP1, PP4, BA1, BS1, BS2, BS3, BS4, BP4 are not met based on absence of qualifying evidence from ClinVar, gnomAD, published literature, and VCEP reference data.6 PP5, BP1, BP2, BP5, BP6, PM6, PP2, and BP3 are not applicable under the TP53 VCEP v2.4.0 specifications. PS5 is not included in the VCEP criteria set. BP7 is not applicable as this is a missense variant.7 Tavtigian point tally: PM2_Supporting (+1) + PP3_Moderate (+2) = 3 points. Per TP53 VCEP v2.4.0 ranges: ≥10 Pathogenic, 6-9 Likely Pathogenic, -1 to 5 Uncertain Significance, -6 to -2 Likely Benign, ≤-7 Benign. Total of 3 points classifies this variant as Uncertain Significance (VUS).8

PM2 + PP3 VUS
2 vcep_pp3_bp4_codesbayesdelspliceai ↗revelcspec ↗
3 cspec ↗pvs1_variant_assessment
4 vcep_functional_worksheetPMID:12826609 ↗PMID:30224644 ↗
5 cspec ↗vcep_functional_worksheet
8 cspec ↗final_classification_framework
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 14 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
PM2_Supporting is met. The variant is absent from gnomAD v2.1 and v4.1, with an allele frequency of 0 in all populations. This satisfies the VCEP PM2_Supporting threshold of an allele frequency less than 0.00003 (0.003%).
gnomAD v2.1: absent (0 alleles)gnomAD v4.1: absent (0 alleles)gnomAD-Canada v1.0: absent (0 alleles)
PP3 moderate Pathogenic
PP3_Moderate is met. The VCEP PP3-BP4-codes.xlsx assigns PP3_moderate for c.293C>G (p.Pro98Arg). This variant has aGVGD Class C65 and a BayesDel score of 0.591769 (≥0.16), satisfying the VCEP PP3_moderate rule. SpliceAI max delta score is 0.00 (<0.2), confirming no predicted splicing impact that would alter the code assignment. REVEL score of 0.955 provides additional in silico support.
PP3-BP4-codes.xlsx: pre-assigned code = PP3_moderateaGVGD: Class C65BayesDel: 0.591769 (≥0.16 VCEP threshold)
Assessed · not applied
Pathogenic
PS1 PS1 is not met.
PS2 PS2 is not met.
PS3 PS3 is not met.
PS4 PS4 is not met.
PM1 PM1 is not met.
PM5 PM5 is not met.
PP1 PP1 is not met.
PP4 PP4 is not met.
Benign
BA1 BA1 is not met.
BS1 BS1 is not met.
BS2 BS2 is not met.
BS3 BS3 is not met.
BS4 BS4 is not met.
BP4 BP4 is not met.
N/A · 10 PVS1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
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
This variant is absent from gnomAD-Canada.
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 (2 clinical laboratories). (ClinVarID = 1444043)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.955. BayesDel score = 0.591769.
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; COSV113304063, n = 3 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
12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. CLINVAR
29979965 ↗ A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. CLINVAR
30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer. CLINVAR
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
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
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR