java variant_variant != mutation

Changes to genes are called mutations.

It's useful to think of mutation as a process that creates genetic variation. We often refer to a mutation as a thing—the genetic variation itself. This approach can be useful when it comes to a gene associated with a disease: the disease allele carries a mutation, a DNA change that compromises the protein's function. However, this approach gives mutation a bad name.

It’s important to remember that losing the function of a gene doesn’t always affect health. For example, most mammals have hundreds of genes that code for olfactory receptors, proteins that help us smell. Losing one of these genes probably doesn’t make all that much difference.

In contrast to variations that cause disease, there are many more examples of variations that are neither good nor bad, but just different—like blood types and eye color. Just like with disease alleles, the process of mutation creates these more neutral variations. But with neutral variations, it can be impossible to tell which allele is the "normal" one that existed first and which is the "mutant"—and the distinction is often meaningless.

A variant call is a conclusion that there is a nucleotide difference vs. some reference at a given position in an individual genome or transcriptome, I Usually accompanied by an estimate of variant frequency and some measure of confidence.