Because of previous reports of two large (>1 Mb), independent de novo deletions spanning this locus 42, we assessed the region surrounding rs10513025 and the entire SEMA5A locus for copy number variation that could either explain or provide independent evidence of the importance of this region to autism using Birdsuite 26 to analyze all Affymetrix 5.0 samples. Birdsuite genotypes previously annotated common copy number polymorphisms 27 and in parallel searches for novel copy number variants using an HMM. Probe coverage in the region was good, with no 50kb window having fewer than 10 probes and an average spacing between probes of 2.5 kb, allowing very good sensitivity for CNVs greater than 25kb. We found no deletions or duplications near this SNP, nor any overlapping the gene SEMA5A. The closest copy number variants upstream and downstream of this SNP appeared to be a rare (~2–3% frequency, previously annotated CNP) 40kb deletion from 288 kb from the 3′ end of SEMA5A, and a rare (~1% frequency, novel) 20kb deletion 356 kb upstream of the 5′ end of SEMA5A. Each of these appeared
