Using large-scale population-based data to improve disease risk assessment of clinical variants

Understanding the disease risk of genetic variants is fundamental to precision medicine. Estimates of penetrance—the probability of disease for individuals with a variant allele—rely on disease-specific cohorts, clinical testing and emerging electronic health record (EHR)-linked biobanks. These data sources, while valuable, each have limitations in quality, representativeness and analyzability. Here, we provide a historical account of the currently accepted pathogenicity classification system and data available in ClinVar, a public archive that aggregates variant interpretations but lacks detailed data for accurate penetrance assessment, highlighting its oversimplification of disease risk. We propose an integrative Bayesian framework that unifies pathogenicity and penetrance, leveraging both functional and real-world evidence to refine risk predictions. In addition, we advocate for enhancing ClinVar with the inclusion of high-priority phenotypes, age-stratified data and population-based cohorts linked to EHRs. We suggest developing a community repository of population-based penetrance estimates to support the clinical application of genetic data.