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).

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).

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).

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).

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.

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.

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.

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.