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.