CNV data from 2,147 European affected subjects and 2,640 European control subjects were analyzed for overlap with genes and loci implicated in ASD and/or ID (results including non-European affected and control subjects are shown in Figure S1). Only CNVs affecting autosomal-dominant and X-linked dominant genes or loci in both genders (132 genes, 56 loci), as well as X-linked recessive genes or loci in males (52 genes, 2 loci), were considered (“all CNV”). Exonic ≥30 kb CNVs affecting an ASD- and/or ID-associated gene or overlapping at least 50% of the target loci were selected for further analysis. Rare CNVs were divided into three categories—pathogenic, uncertain clinical significance, or benign—without regard to affected status.