Specifications of the ACMG/AMP variant interpretation guidelines for germline TP53 variants

Abstract

Germline pathogenic variants in TP53 are associated with Li-Fraumeni syndrome, a cancer predisposition disorder inherited in an autosomal dominant pattern associated with a high risk of malignancy, including early-onset breast cancers, sarcomas, adrenocortical carcinomas, and brain tumors. Intense cancer surveillance for individuals with TP53 germline pathogenic variants is associated with reduced cancer-related mortality. Accurate and consistent classification of germline variants across clinical and research laboratories is important to ensure appropriate cancer surveillance recommendations. Here, we describe the work performed by the Clinical Genome Resource TP53 Variant Curation Expert Panel (ClinGen TP53 VCEP) focused on specifying the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification to the TP53 gene. Specifications were developed for 20 ACMG/AMP criteria, while nine were deemed not applicable. The original strength level for the 10 criteria was also adjusted due to current evidence. Use of TP53-specific guidelines and sharing of clinical data among experts and clinical laboratories led to a decrease in variants of uncertain significance from 28% to 12% compared with the original guidelines. The ClinGen TP53 VCEP recommends the use of these TP53-specific ACMG/AMP guidelines as the standard strategy for TP53 germline variant classification.

Keywords: TP53; cancer; pathogenic variant; variant curation.

Figure 1.

Flow chart for the specifications of PS3 and BS3 criteria. Non-functional (Kato) = median transactivation activity ≤20%; Partially functional (Kato) = median transactivation activity >20 and ≤75%; Functional/Supertrans (Kato) = median transactivation activity >75%; DNE+LOF (Giacomelli) = p53WTNutlin3 Z-score ≥ 0.61 and Etoposide Z-score ≤ −0.21 = noDNE+noLOF (Giacomelli) = p53WTNutlin3 Z-score < 0.61 and Etoposide Z-score > −0.21. Other assays are available in IARC TP53 Database or original publications, and include in vitro growth assays in H1299 human cells from Kotler et al., (2018) with RFS score > −1.0 for LOF and RFS score < −1.0 for noLOF; or colony formation assays, growth suppression assays, apoptosis assays, tetramer assays, knock-in mouse models. * If a variant does not match any of the possibilities shown, it is considered to have “no evidence to review” and no functional criterion can be applied. Abbreviations: DNE = Dominant-negative effect; LOF = Loss-of-function.

Figure 2.

Variant classifications for 43 pilot TP53 variants in ClinVar, from the nominating expert(s), biocurators using the original ACMG/AMP guidelines, and the TP53-specific guidelines. Abbreviations: B = Benign, LB = Likely benign, VUS = Variant of uncertain significance, LP = Likely pathogenic, P = Pathogenic, Conflicting = Clinically relevant conflicting interpretations of pathogenicity, and NA = Not Available.