This dataset comprises CNV calls from Whole Exome Sequencing (WES) across multiple distinct Alzheimer’s Disease (AD) sequencing projects, including the discovery and replication ADSP family datasets, the ADSP case-control dataset, and the ADNI dataset. A total of 16,201 samples were processed for CNV detection using CANOES software, and the resulting files are formatted as BED files. Additionally, the dataset includes target definition files specifying the chromosomal positions used, as well as batch files defining the reference genome, the target file applied, and subject mappings.