We find 1,492 CNVs in 1,400 individuals within 45 known genomic disorder regions (Table 1, Supplementary Table 5). Among these, deletions are twice as common (n = 954 deletions vs. 538 duplications) and show greater average penetrance (96.3%) when compared to duplications (94.3%). We note that “classic,” phenotypically well-defined syndromes known to result from CNVs (e.g. Smith-Magenis, Williams syndrome, etc.) are underrepresented here relative to other cohorts of individuals with similar phenotypes (Supplementary Table 6), suggesting that our estimate of CNV burden in ID/DD is not upwardly biased by ascertainment for known CNV carriers.
