Genetics · BEGINNER LESSON
Alternative allele
An alternative allele is any DNA base or sequence version at a specific genomic location that is not the reference allele. A variant can have one or more alternative alleles, and the alternative allele is not the same thing as the minor allele.
What it is
An allele is one of the possible DNA versions found at a particular genomic location. In genome-scale data, the reference allele is the version shown in the reference genome, and the alternative allele is any other base or sequence observed at that location. A single variant can have more than one alternative allele. This label describes how a DNA version is named, not whether it is common, rare, or harmful.
[1] 1.3 [2] 1 [3] What are variants, alleles and haplotypes? | Human genetic variation
What is measured
Researchers measure which allele is present at a site in a person or in a population, and they can count how often each allele appears. That is why terms such as minor allele frequency exist: minor allele means the less common allele in a population, while alternative allele only means it differs from the reference genome. These are different labels, so a variant’s alternative allele may be common or rare.
[1] 1.3 [2] 1 [3] What are variants, alleles and haplotypes? | Human genetic variation
How the labels work
At one site, one allele is called the reference because it matches the reference genome. Any other observed version at that same site is an alternative allele. This naming is practical for data analysis, but it depends on the chosen reference genome. The same site can also be described with other systems, such as minor/major or ancestral/derived, but those labels answer different questions.
[1] 1.3 [3] What are variants, alleles and haplotypes? | Human genetic variation
Why the distinction matters
The alternative allele is not automatically the minor allele, and it is not automatically linked to a trait. In some cases there can be more than one alternative allele, so the site may have several non-reference versions. Because the reference genome is just one genome used as a standard, the reference label can be arbitrary for some sites.
[1] 1.3 [3] What are variants, alleles and haplotypes? | Human genetic variation
Limitations and cautions
Different naming systems can disagree. Minor/major labels depend on frequency in a population and can switch when frequencies are close to 50%. Ancestral/derived labels depend on inference about evolutionary history and can be uncertain. The alternative allele label avoids those specific problems, but it only tells you which version is not in the reference genome, not what that version does biologically.
[1] 1.3 [3] What are variants, alleles and haplotypes? | Human genetic variation
SEE THE IDEA
How a variant gets an alternative-allele label
A specific position in DNA where variation can occur.
The version found in the reference genome at that position.
Any other observed version at the same position.
Other systems may call the allele minor, major, ancestral, or derived based on different criteria.
At one genomic location, compare the observed DNA version to the reference genome; any non-reference version is labeled as an alternative allele, while other naming systems may classify it differently.
The same DNA change can be named by reference status, population frequency, or evolutionary history, depending on the question being asked.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.