Genomic variation definitions. (A) A single nucleotide polymorphism (SNP) occurs as a result of a single base substitution at an individual site in the DNA sequence along the chromosome. Nonsynonymous coding SNPs occur in the coding region of a gene where the alternate SNP allele results in the coding of a different amino acid. (B) A deletion is the loss/absence of DNA sequence. (C) An inversion is a rearrangement causing a segment of DNA to be present in reverse orientation. (D) A copy number variant (CNV) is a segment of DNA that is 1 kb or larger and is present at a variable copy number in comparison with a reference genome. CNVs can be either deletion variants where there is loss of copy number relative to the reference sequence or multicopy duplications where there is gain of copy number relative to the reference sample. (E) A segmental duplication is a segment of DNA at least 1 kb in size that occurs in 2 or more copies per haploid genome, with the different copies sharing at least 90% sequence identity. (F) A large-scale copy number variant is a CNV that involves a segment of DNA more than 50 kb in size.