The present study aimed to identify the mutation causing an atypical syndrome. High-resolution single nucleotide polymorphism (SNP) arrays are considered to be a major detection method for submicroscopic chromosomal rearrangements smaller than 5 Mb in size. Genomic DNA samples of the patient and his parents were converted to a final concentration of 50 ng/ml. The Illumina BeadScan genotyping system and the HumanOmni1‑Quad Chip were employed to obtain the signal intensities of SNP probes. The patient presented with congenital heart disease, autism, mental retardation, growth retardation, hypercalcemia, nephroliths and cleft palate. The karyotypes of the patient and his parents were normal. The present study employed high‑resolution SNP arrays to analyze the whole genome for copy number variations (CNVs). A total of 309 CNVs were discovered. A de novo 1.5 Mb gain of chromosome 7q11.23 (Chr7: 72,357,322‑73,856,472) was identified following exclusion of CNVs presented in the Database of Genomic Variants. In conclusion, to the best of our knowledge, the current study describes the first case of a patient presenting with Williams‑Beuren syndrome alongside supravalvular aortic stenosis, autism and cleft palate, and identifies an atypical deletion at 7q11.23.