Variant classification summary

NM_000546.5:c.520A>T

TP53 · NP_000537.3:p.(Arg174Trp) · NM_000546.5

GRCh37: chr17:7578410 T>A · GRCh38: chr17:7675092 T>A

Gene: TP53 Transcript: NM_000546.5

Final call

VUS

PS3 strong PM2 supporting BP4 supporting

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Arg174Trp)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PS3 (strong) is met: R174W is non-functional in the Kato et al. assay and demonstrates loss of function across all eligible functional assays (Giacomelli, Kotler, Kawaguchi), per the TP53 VCEP Functional-worksheet pre-adjudicated assignment.

2

PM2_Supporting is met: the variant is absent from gnomAD v2.1 and v4.1, with an allele frequency below the VCEP threshold of 0.00003.

3

BP4_Supporting is met: the VCEP PP3-BP4-codes spreadsheet assigns BP4 to c.520A>T based on BayesDel score 0.149306 and SpliceAI max delta 0.0, indicating no predicted deleterious effect from in silico tools.

4

PM1 is not met: codon 174 is not among the VCEP-defined hotspot codons (175, 245, 248, 249, 273, 282), and the variant is not listed in cancerhotspots.org.

5

PS1 is not met: no alternate nucleotide change producing the same Arg174Trp amino acid substitution has been classified as Pathogenic or Likely Pathogenic by the TP53 VCEP.

6

PS4, PS2, PP1, PP4, BS2, and BS4 remain not assessed due to absence of proband-level clinical, segregation, or population phenotype data.

7

Applying the Tavtigian 2020 Bayesian point system: PS3 (+4) + PM2_Supporting (+1) + BP4_Supporting (-1) = 4 points. This falls within the VUS range (>= -1 and <= 5 points).

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 4, which maps to VUS under the specified Tavtigian-style ranges.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 applies only to null variants (nonsense, frameshift, canonical splice sites, CNVs); NM_000546.5:c.520A>T is a missense variant (p.Arg174Trp) and does not fall into any PVS1-eligible variant bucket per the TP53 VCEP PVS1 flowchart.
PS1	Not met	PS1 requires a different nucleotide change producing the same amino acid change (Arg174Trp) previously classified as Pathogenic or Likely Pathogenic by the TP53 VCEP. No such variant has been identified in the VCEP materials or ClinVar for this codon.
PS2	Not assessed	No proband data with de novo confirmation (maternity and paternity) or LFS cancer point scoring available for this variant.
PS3	Met	TP53 VCEP Functional-worksheet (Supplementary Table S3) directly assigns PS3 to p.Arg174Trp (R174W). R174W is non-functional in the Kato et al. assay (PMID:12826609) and demonstrates loss of function across all other eligible functional assays (Giacomelli, Kotler, Kawaguchi), meeting the VCEP PS3 rule: non-functional on Kato data AND LOF by the majority of other eligible assays.	vcep_functional_worksheet PMID:12826609 PMID:30224644 PMID:29979965
PS4	Not assessed	No proband-level LFS cancer data available for PS4 point scoring. The ClinVar record (VCV000964680) contains a single submission classified as Uncertain Significance with no proband phenotype details.	clinvar
PS5	N/A	PS5 is not a defined criterion in the TP53 VCEP framework. The VCEP uses a combined PS2/PM6 rule with point-based scoring for de novo observations; PS5 as a separate criterion is not recognized.
PM1	Not met	Codon 174 is not among the VCEP-defined TP53 hotspot codons (175, 245, 248, 249, 273, 282). The variant is not listed in cancerhotspots.org, so the supporting-level rule (2-9 somatic occurrences for same amino acid change) cannot be applied via that pathway. Although COSMIC reports 28 somatic occurrences and the residue is a statistically significant hotspot, the VCEP PM1 rule is restricted to the specified codons or cancerhotspots-listed variants.
PM2	Met	Variant is absent from gnomAD v2.1 and v4.1, meeting the TP53 VCEP PM2_Supporting threshold of allele frequency < 0.00003 (0.003%).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not assessed	PM5 requires a different missense variant at the same residue (Arg174) previously classified as Pathogenic or Likely Pathogenic by the TP53 VCEP. While multiple other missense changes at codon 174 exist (R174G, R174K, R174M, R174S, R174T in PP3-BP4-codes; R174A/C/E/I/N/P/Q/V in Functional-worksheet), their VCEP clinical classifications (not just functional codes) are needed to apply PM5.
PM6	N/A	PM6 is explicitly marked as Not Applicable by the TP53 VCEP; de novo observations are assessed under the combined PS2 point-based rule instead.
PP1	Not assessed	No cosegregation data available. The VCEP PP1 rule requires 3-4 meioses for Supporting, 5-6 for Moderate, or >=7 for Strong.
PP2	N/A	PP2 is explicitly marked as Not Applicable by the TP53 VCEP.
PP3	Not met	TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2) assigns BP4 (not PP3) to c.520A>T. BayesDel score 0.149306 is below the 0.16 threshold required for PP3_Supporting (aGVGD Class C25-C55 AND BayesDel >= 0.16), and the variant is Class C35, not C65. SpliceAI max delta 0.0 confirms no predicted splicing impact.	vcep_pp3_bp4_codes revel bayesdel spliceai
PP4	Not assessed	No variant allele fraction (VAF) data or specific phenotype observations available. The VCEP PP4 rule requires observation of the variant at VAF 5-35% (Supporting) or >=2 independent observations at VAF 5-25% (Moderate).
PP5	N/A	PP5 is explicitly marked as Not Applicable by the TP53 VCEP as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
BA1	Not met	Variant is absent from gnomAD. Does not meet the TP53 VCEP BA1 threshold of filtering allele frequency >= 0.001 (0.1%) in any continental subpopulation.	gnomad_v2 gnomad_v4
BS1	Not met	Variant is absent from gnomAD. Does not meet the TP53 VCEP BS1 threshold of filtering allele frequency >= 0.0003 (0.03%) in any continental subpopulation.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available on unrelated females >=60 years of age without cancer. The VCEP BS2 rule requires 2-3 such individuals for Supporting, 4-7 for Moderate, or >=8 for Strong.
BS3	Not met	TP53 VCEP Functional-worksheet assigns PS3 (not BS3) to R174W. The variant is non-functional in Kato assay with LOF across all eligible assays, which is the opposite of what BS3 requires (functional or partially functional with no LOF evidence).	vcep_functional_worksheet
BS4	Not assessed	No segregation data available. The VCEP BS4 rule requires lack of segregation in affected family members diagnosed with LFS-associated cancers.
BP1	N/A	BP1 is explicitly marked as Not Applicable by the TP53 VCEP; truncating variants account for only a portion of disease-causing variants in TP53.
BP2	N/A	BP2 is explicitly marked as Not Applicable by the TP53 VCEP.
BP4	Met	TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2) directly assigns BP4 to c.520A>T. BayesDel score 0.149306 is < 0.16 and > -0.008 with aGVGD Class C35 (not C65), and SpliceAI max delta 0.0 confirms no predicted splicing impact, meeting the VCEP BP4_Supporting rule exactly.	vcep_pp3_bp4_codes bayesdel spliceai
BP5	N/A	BP5 is explicitly marked as Not Applicable by the TP53 VCEP.
BP6	N/A	BP6 is explicitly marked as Not Applicable by the TP53 VCEP as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants. NM_000546.5:c.520A>T is a missense variant (p.Arg174Trp) and is not eligible for BP7.

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