A genomic foundation model for interpreting human genetic diversity

Interpreting human genomes requires models that recognize shared biological functions while accounting for variation underlying traits, disease susceptibility and adaptation. Here we present hEVO, a genomic foundation model trained on 4.784 billion distinct haplotype sequences reconstructed from whole genome sequencing (WGS) data for 63,809 individuals selected from 550,237 samples across eight cohorts. Pretraining integrates shared sequence features and naturally occurring allelic differences without clinical or functional labels. Against representatives of the Evo 2, NT, GPN and other genomic model families, hEVO ranked first in 18 of 19 primary comparisons spanning functional annotation, variant interpretation and human evolution. Its pretrained allele scores generalized across all six complementary variant benchmarks without task-specific training, achieving the highest performance across clinical pathogenicity, fine-mapped causal variants and experimentally measured regulatory effects. Retrospective ClinVar reclassification further demonstrated improved identification of pathogenic classifications later downgraded, supporting reassessment of earlier clinical interpretations. Predictive strengths extended to ancestry inference, human accelerated sequences and preference for reported selected alleles. This breadth was achieved with substantially fewer parameters than billion-parameter comparators and low inference overhead in the evaluated workloads. These findings establish human haplotype diversity as a source of transferable biological information for interpreting both the disruption of genome function and the variation retained during human evolution.