variant

BioCodeKb - Bioinformatics Knowledgebase

The term variant can be used to describe an alteration that may be benign, pathogenic or of unknown significance. The term variant is increasingly being used in place of the term mutation. Variation, in biology, any difference between cells, individual organisms, or groups of organisms of any species caused either by genetic differences (genotypic variation) or by the effect of environmental factors on the expression of the genetic potentials (phenotypic variation). Variation may be shown in physical appearance, metabolism, fertility, mode of reproduction, behaviour, learning and mental ability and other obvious or measurable characters.


We get our genes from our parents, which is why we and our siblings look similar to them and each other. Our genes have alleles, which are different forms of the same gene. Alleles are like a code for our body that determine hair color and eye color, height, and other genetic features.


Genetic variation is the variation in alleles and genes, both within and among populations. Think of a population as a family unit. Within our family of closely-related individuals there is genetic variation. Within a neighborhood, there are many families, and so there is also genetic variation among that larger group.


Genetic variation can be identified through either continuous or discrete traits. Continuous traits are traits that vary continuously, such as height and weight. Discrete traits are traits that can only be measured discretely, such as tongue rolling, we either can or can't do this.


Sources of variation

99.5% of all DNA is shared across all humans, it is the 0.5% that makes all the difference. Genetic variations, or variants, are the differences that make each person’s genome unique. DNA sequencing identifies an individual’s variants by comparing the DNA sequence of an individual to the DNA sequence of a reference genome maintained by the Genome Reference Consortium (GRC).

  • A mutation is simply a change in the DNA. Mutations themselves are not very common and are usually harmful to a population. Because of this, mutations are usually selected against through evolutionary processes.

  • Single nucleotide polymorphisms (“SNPs”, pronounced “snips”) are DNA sequence variations that occur when a single nucleotide differs from the reference DNA sequence. To qualify as a SNP, the variant must be present in at least 1% of the population.

  • Insertions are when additional nucleotides inserted in a DNA sequence, relative to the reference sequence.

  • Deletions are when there are missing nucleotides, relative to the reference sequence.

  • Substitutions are when multiple nucleotides are altered from the reference sequence.

  • Structural variants are changes where large sections of a chromosome or even whole chromosomes are duplicated, deleted or rearranged in some manner.


The American College of Medical Genetics and Genomics (ACMG) has developed guidelines for the classification of DNA sequence variants:

  • Pathogenic - a sequence variant that is previously reported and is a recognized cause of the disorder.

  • Likely Pathogenic – a sequence variant that is previously unreported and is of the type which is expected to cause the disorder.

  • VUS (Variant of Unknown Significance) – a sequence variant that is previously unreported and is of the type which may or may not be causative of the disorder.

  • Likely Benign – a sequence variant that is previously unreported and is probably not causative of disease.

  • Benign – a sequence variant is previously reported and is a recognized neutral variant.

  • A sequence variant that is previously not known or expected to be causative of disease, but is found to exist in people with a particular disease or disorder.

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