> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter/terminology.md).

# Terminology

A quick reference for terms used throughout the Variant Interpreter.

* **Allele**: one of the two copies of a gene or position; one inherited from each parent.
* **Autosomal recessive**: a condition that appears only when both copies of a gene are affected.
* **Biallelic**: both copies of a gene are affected (homozygous or compound heterozygous).
* **Carrier**: someone with one affected copy who is typically unaffected.
* **Compound heterozygote**: two different affecting variants, one on each copy of a gene.
* **Copy-number variant (CNV)**: a change in the number of copies of a region.
* **Consequence**: the predicted functional effect of a variant (e.g. missense, frameshift).
* **Haplotype**: the set of variants on one physical copy of a chromosome.
* **Imprinting**: normal expression of a gene from only one parental copy; loss of imprinting disrupts this.
* **Indel**: a short insertion or deletion.
* **Methylation**: a chemical mark on DNA that can switch genes on or off; read directly from long-read data.
* **Paralog**: a near-identical copy of a gene elsewhere in the genome.
* **Penetrance**: the proportion of people with a variant who show the condition.
* **Phasing**: determining which variants lie on the same physical chromosome copy.
* **Population/allele frequency**: how common a variant is in reference populations; used to filter out common variants.
* **Segmental duplication**: a genomic region with a near-identical copy elsewhere.
* **Small variant**: an SNV or short indel (< 50 bp).
* **Structural variant (SV)**: a larger rearrangement, typically ≥ 50 bp.
* **Tandem repeat**: a short motif repeated back-to-back; expansions can cause disease.

## Platform terms

* **Workspace**: the tenant/environment you select after logging in; contains the samples you can access.
* **Instrument**: the sequencing instrument whose samples are listed on the Data Page; you select one to see its samples.
* **Sample**: one individual's sequenced data; the unit you open in the interpreter.
* **Case**: a sample's interpretation session, ending in a signed report.
* **Priority findings**: the variants the interpreter surfaces on the Summary tab as most likely pathogenic.
* **Review analysis**: the action on a succeeded workflow run that opens the sample in the Variant Interpreter.
* **Sample drawer**: a slide-out panel, available on every screen, showing the sample's details, pedigree, and workflow history.


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