NM_000546.5:c.833C>G (p.Pro278Arg) is a missense variant in TP53 exon 8, absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF=6.2e-7, 1/1,614,022 alleles).

PS3 (Strong) is met: the variant is Non-functional in the Kato et al. functional assay AND demonstrates loss of function by the majority of other eligible assays (Giacomelli: LOF, Kotler: LOF, Funk: noLOF), per the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3).

PM1 (Moderate) is met: codon 278 is a statistically significant hotspot residue in cancerhotspots.org, and the Pro278Arg change has 82 somatic occurrences in COSMIC, far exceeding the VCEP threshold of >=10 for PM1_Moderate.

PM2 (Supporting) is met: the variant allele frequency in gnomAD v4.1 (6.2e-7) is well below the VCEP PM2_Supporting threshold of 0.00003, with no genetic ancestry group exceeding 0.00004.

PP3 (Moderate) is met per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2): aGVGD class C65 with BayesDel score 0.607821 (>=0.16), and SpliceAI predicts no splicing impact (max delta 0.00).

Multiple criteria remain unassessed due to absent data: PS1 (requires VCEP classification of alternate nucleotide change c.833C>A for same amino acid P278R), PS2 (no de novo report with confirmed parentage), PS4 (germline proband counts unavailable), PM5 (formal VCEP classifications for codon 278 comparators needed), PP1 (no cosegregation data), PP4 (no VAF data), BS2 (no data on elderly unaffected carriers), and BS4 (no lack-of-segregation reports).

Applying the TP53 VCEP v2.4.0 Tavtigian point system: PS3=4 + PM1=1 + PM2_Supporting=0.5 + PP3_Moderate=1 = 6.5 points, which falls in the Likely Pathogenic range (6-9 points).

This variant has been reported in ClinVar with conflicting classifications: Uncertain significance (3 clinical laboratories), Likely pathogenic (1), and Pathogenic (1). (ClinVar Variation ID: 376644)