Variant classification summary

NM_000546.5:c.845G>T

TP53 · NP_000537.3:p.(Arg282Leu) · NM_000546.5

GRCh37: chr17:7577093 C>A · GRCh38: chr17:7673775 C>A

Gene: TP53 Transcript: NM_000546.5

Final call

VUS

PM1 moderate PM2 supporting PP3 moderate BS3 strong

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Arg282Leu)

gnomAD AF

3.0979817268645824e-06 (v4.1)

ClinVar

Uncertain Significance

OncoKB

Likely Neutral

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.5:c.845G>T (p.Arg282Leu) is a missense variant in exon 8 of TP53, assessed under the ClinGen TP53 Variant Curation Expert Panel specifications version 2.4.0 (Tavtigian point-based framework).

2

This variant affects codon 282, a well-established mutational hotspot within the DNA-binding domain explicitly listed in the TP53 VCEP PM1 rule. The residue is a statistically significant cancer hotspot with 10 somatic occurrences in COSMIC, satisfying PM1 at moderate strength (+2 points).

3

The variant is extremely rare in population databases: gnomAD v4.1 reports an allele frequency of 3.10×10⁻⁶ (5/1,613,954 alleles; grpmax FAF=7.9×10⁻⁷), and it is absent from gnomAD v2.1. All subpopulation frequencies are well below the TP53 VCEP PM2_Supporting cutoff of <0.003%, satisfying PM2 at supporting level (+1 point).

4

In silico predictors support a deleterious effect: aGVGD Class C65 with BayesDel score 0.360452 and REVEL score 0.898. Per the TP53 VCEP PP3-BP4-codes worksheet, this variant is assigned PP3_moderate (+2 points). SpliceAI predicts no splicing impact (max delta=0.00).

5

Functional data from the TP53 VCEP Functional-worksheet demonstrates that p.Arg282Leu is functional in the Kato assay and shows no loss of function in Giacomelli, Kotler, and Kawaguchi assays. This satisfies BS3 at strong benign strength (−4 points): functional on Kato AND no LOF by the majority of eligible assays.

6

The variant has been reported in ClinVar as Uncertain Significance by 6 clinical laboratories and as Uncertain Significance by the ClinGen TP53 Variant Curation Expert Panel (ClinVar ID: 182938). No proband data meeting Li-Fraumeni syndrome criteria was available for PS4 assessment.

7

No de novo observations, cosegregation data, VAF data, or BS2/BS4 evidence was identified for this variant. PVS1 is not applicable to this missense variant. PS1 has no alternative nucleotide change comparator. PM5 requires curator review of VCEP classifications for comparator codon 282 variants.

8

Final Tavtigian point total: PM1_Moderate (+2) + PM2_Supporting (+1) + PP3_Moderate (+2) + BS3_Strong (−4) = +1 point. This falls within the Uncertain Significance range (−1 to +5) per the TP53 VCEP v2.4.0 Tavtigian point-based rules. The classification is consistent with the ClinGen TP53 VCEP expert panel determination of Uncertain Significance for this variant.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 1, 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
BP3	N/A	In-frame deletions/insertions in repetitive region — not relevant to a single-nucleotide missense substitution.
PM3	N/A	Recessive disorder criterion — not applicable to TP53, a tumor suppressor with autosomal dominant inheritance.
PM4	N/A	Non-repeat in-frame deletion/insertion criterion — this is a missense substitution, not an in-frame indel.
PVS1	N/A	Missense variant; PVS1 is reserved for null variants (nonsense, frameshift, canonical splice site) per both ACMG/AMP 2015 and TP53 VCEP v2.4.0 PVS1 flowchart. This variant does not fall into any PVS1 bucket: it is neither a null variant nor a canonical splice alteration.	cspec pvs1_generic_framework
PS1	N/A	PS1 requires a different nucleotide change producing the same amino acid substitution (p.Arg282Leu) previously classified as P/LP per VCEP. The codon is CGG (Arg). c.845G>A yields CAG (Gln) and c.845G>C yields CCG (Pro); no alternative nucleotide substitution at c.845 produces leucine. Therefore no same-amino-acid comparator exists.	cspec
PS2	Not met	No confirmed de novo observation with confirmed maternity/paternity has been identified for this variant. The exploratory search referenced an unverifiable source (PMID not found in PubMed). ClinVar submissions do not include de novo reports for this variant.	clinvar
PS3	Not met	Per the TP53 VCEP Functional-worksheet (Supplementary Table S3), the p.Arg282Leu substitution is functional in the Kato assay and demonstrates no loss of function across Giacomelli, Kotler, and Kawaguchi assays. The pre-assigned VCEP code is BS3 (benign functional evidence), not PS3. The variant retains wild-type-like function, so pathogenic functional evidence (PS3) is not met.	vcep_functional_worksheet
PS4	Not met	No verified proband data meeting Li-Fraumeni syndrome criteria is available to assign PS4 points. The ClinGen TP53 Variant Curation Expert Panel classified this variant as Uncertain Significance (ClinVar ID 182938), indicating insufficient proband evidence to support PS4. The exploratory search referenced unverifiable sources. COSMIC reports 10 somatic occurrences, but somatic data does not directly support germline PS4 per VCEP specifications.	clinvar
PS5	N/A	PS5 is not used by the TP53 VCEP and is not included in the v2.4.0 specifications. Per ClinGen SVI recommendations, this criterion has been functionally superseded and is not applied in current variant interpretation frameworks.	cspec
PM1	Met	This missense variant affects codon 282 (p.Arg282), which is explicitly listed in the TP53 VCEP PM1 rule as a moderate-strength hotspot codon (alongside codons 175, 245, 248, 249, 273). Additionally, the residue is a statistically significant cancer hotspot (cancerhotspots.org), and COSMIC records 10 somatic occurrences at this amino acid change, independently satisfying the PM1_Moderate threshold (≥10 somatic occurrences for the same amino acid change).	cspec
PM2	Met	This variant is extremely rare in population databases. In gnomAD v4.1, the total allele frequency is 3.10×10⁻⁶ (5/1,613,954 alleles), with a grpmax filtering allele frequency of 7.9×10⁻⁷. The highest subpopulation frequency is in East Asian (2.23×10⁻⁵; 1/44,858 alleles). Both the total AF and subpopulation AF are well below the TP53 VCEP PM2_Supporting cutoff of <0.00003 (0.003%) total and <0.00004 (0.004%) per genetic ancestry group. The variant is absent from gnomAD v2.1. No founder-effect populations are implicated.	gnomad_v4 gnomad_v2 cspec
PM5	Not assessed	Multiple different missense variants exist at codon 282 (R282G, R282P, R282W — all assigned PS3 in the VCEP functional worksheet). However, PM5 per TP53 VCEP requires comparator variants to be previously classified as Pathogenic or Likely Pathogenic according to the TP53 VCEP specifications. Without access to the VCEP classification database to confirm the final classification status of comparator variants at codon 282 (as distinct from functional evidence alone), PM5 cannot be definitively applied. This requires curator review of VCEP classifications for R282G, R282P, R282W, and other codon 282 variants.	cspec vcep_functional_worksheet
PM6	N/A	PM6 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion is not used for TP53 variant interpretation per ClinGen SVI VCEP Review Committee guidance.	cspec
PP1	Not met	No verified cosegregation data is available for this variant. The exploratory search referenced an unverifiable source (non-existent PMID). No family studies demonstrating cosegregation of this variant with Li-Fraumeni syndrome phenotypes were identified in the evidence packet.
PP2	N/A	PP2 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion (missense in gene with low rate of benign missense variation) is not used for TP53 per ClinGen SVI guidance.	cspec
PP3	Met	Per the TP53 VCEP PP3-BP4-codes worksheet (Supplementary Table S2), this variant is assigned aGVGD Class C65 with BayesDel score 0.360452 and the pre-computed code PP3_moderate. The VCEP PP3 rule specifies that aGVGD Class C65 with BayesDel ≥0.16 qualifies for PP3 at moderate strength. SpliceAI predicts no splicing impact (max delta = 0.00), so the in silico assessment proceeds via the missense pathway without splicing considerations. REVEL score (0.898) independently supports a deleterious prediction.	vcep_pp3_bp4_codes bayesdel revel spliceai cspec
PP4	Not met	PP4 per TP53 VCEP requires observation of the variant at low variant allele fraction (VAF 5-35%) in blood, indicative of somatic mosaicism or clonal hematopoiesis. No VAF data is available for this variant in the evidence packet. This criterion cannot be assessed without allele-specific quantification from clinical testing data.	cspec
PP5	N/A	PP5 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	The variant is extremely rare, not common. gnomAD v4.1 grpmax filtering allele frequency is 7.9×10⁻⁷, far below the TP53 VCEP BA1 standalone benign threshold of ≥0.001 (0.1%). The variant is absent from gnomAD v2.1. BA1 is not met.	gnomad_v4 gnomad_v2 cspec
BS1	Not met	The variant's population frequency is too low to meet BS1. gnomAD v4.1 grpmax filtering allele frequency is 7.9×10⁻⁷, far below the TP53 VCEP BS1_Strong threshold of ≥0.0003 (0.03%). No genetic ancestry group (excluding founder populations) has ≥2 alleles above the BS1 cutoff.	gnomad_v4 gnomad_v2 cspec
BS2	Not met	BS2 per TP53 VCEP requires observations of the variant in unrelated females aged ≥60 years without cancer, from a single source. No such data is available in the evidence packet. gnomAD does not provide age or cancer phenotype data for variant carriers.	cspec
BS3	Met	Per the TP53 VCEP Functional-worksheet (Supplementary Table S3), the p.Arg282Leu variant is functional in the Kato et al. assay and demonstrates no loss of function in the Giacomelli, Kotler, and Kawaguchi assays (all noLOF). This satisfies the TP53 VCEP BS3_Strong rule: 'Functional on Kato et al. data AND no loss of function (LOF) by the majority of available eligible assays.' The variant retains wild-type-like protein function across multiple orthogonal functional assays, providing strong evidence for a benign functional effect.	vcep_functional_worksheet cspec
BS4	Not met	BS4 per TP53 VCEP requires lack of segregation in affected family members (family members diagnosed with LFS-associated cancers who do not carry the variant). No verified segregation data — either for or against — is available for this variant. The exploratory search referenced an unverifiable source.	cspec
BP1	N/A	BP1 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion (missense variant in a gene where primarily truncating variants cause disease) is not used for TP53 per ClinGen SVI guidance.	cspec
BP2	N/A	BP2 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion (observed in trans with a pathogenic variant for a fully penetrant dominant disorder) is not used for TP53.	cspec
BP4	Not met	The variant's BayesDel score (0.360452) is above the BP4 threshold (<0.16). Per the TP53 VCEP PP3-BP4-codes worksheet, this variant is assigned PP3_moderate (not BP4). The aGVGD class is C65, which per the VCEP flowchart precludes BP4 application. SpliceAI predicts no splicing impact (max delta=0.00), but the missense in silico scores are in the pathogenic range, not benign.	vcep_pp3_bp4_codes bayesdel cspec
BP5	N/A	BP5 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion (variant found in a case with an alternate molecular basis for disease) is not used for TP53.	cspec
BP6	N/A	BP6 is marked as Not Applicable by the TP53 VCEP v2.4.0 specifications. This criterion (reputable source reports variant as benign) is not for use per ClinGen SVI VCEP Review Committee guidance.	cspec
BP7	N/A	BP7 is applicable only to synonymous (silent) and intronic variants per the TP53 VCEP PP3/BP4/BP7 flowchart. This is a missense variant (c.845G>T, p.Arg282Leu) and does not qualify for BP7 evaluation.	cspec vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7

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