We developed an automated program to scan the data for inconsistencies in clinical interpretation for two or more reported genomic imbalances that overlapped in length by more than 50%, but that were classified differently (as pathogenic, VOUS, or benign). This program flagged the genomic regions in which there was inconsistent annotation of CNVs, and these CNVs were subsequently reviewed and, where appropriate, assigned a single classification. For cases with complex rearrangements involving several CNVs, the interpretation was based on each individual CNV. The reported CNVs from this study are included in Supplemental Table 4 and were submitted to dbVar (nstd37). The number of genes was assessed by counting partial and whole genes included in the region based on the UCSC known gene track.
