Hematopoietic mosaic chromosomal alterations are pleiotropic drivers of inflammaging, multimorbidity, and mortality.

Mosaic chromosomal alterations (mCAs) are a prevalent but poorly understood form of clonal hematopoiesis (CH). Whether mCAs contribute to disease independently of CHIP, and whether their large-scale genomic effects can be resolved to actionable targets, remain unknown. In 452,594 UK Biobank participants, we show that mCAs confer multimorbidity and mortality risk independent of CHIP. Notably, mCA-CHIP co-occurrence defines a very high-risk clonal state with synergistically elevated mortality, identifying a population not captured by CHIP screening alone. To resolve large mCAs to specific disease mechanisms, a cytoband-level mapping framework was developed that links mCAs to discrete genomic loci and candidate effector genes. Functional validation using single-cell transcriptomics and mouse models prioritized MYC (chr8 gain) and S100A9 (chr1 gain) as key drivers of systemic inflammation and multiorgan pathology. These findings establish mCAs as independent, synergistic, and genetically-resolvable drivers of age-related disease, with immediate implications for screening, risk stratification, and therapeutic development.