In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome and is present in a sufficiently large fraction of the population (1% or more). Single nucleotide substitutions with an allele frequency of less than 1% are called "single-nucleotide variants", not SNPs.

For example, at a specific base position in the human genome, the G nucleotide may appear in most individuals, but in a minority of individuals, the position is occupied by an A. This means that there is a SNP at this specific position, and the two possible nucleotide variations – G or A – are said to be the alleles for this specific position.

SNPs pinpoint differences in our susceptibility to a wide range of diseases, for example age-related macular degeneration (a common SNP in the CFH gene is associated with increased risk of the disease) or nonalcoholic fatty liver disease (a SNP in the PNPLA3 gene is associated with increased risk of the disease). The severity of illness and the way the body responds to treatments are also manifestations of genetic variations caused by SNPs. For example, the APOE E4 allele that is determined by two common SNPs, rs429358 and rs7412, in the APOE gene is not only associated with increased risk for Alzheimer’s disease but also younger age at onset of the disease.

A single-nucleotide variant (SNV) is a general term for single nucleotide change in DNA sequence. So a SNV can be a common SNP or a rare mutation, and can be germline or somatic and can be caused by cancer, but a SNP has to segregate in a species' population of organisms. SNVs also commonly arise in molecular diagnostics such as designing PCR primers to detect viruses, in which the viral RNA or DNA sample may contain SNVs.