> 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/reviewing-variants/annotation-panels.md). # Annotation panels When you open a variant, the interpreter enriches it with evidence from external reference databases. Each source appears as its own panel on the variant, giving you the population and clinical context you need to classify it without leaving Workbench. Every panel links out to the source record so you can drill in when you need to. If a source can't be reached, its panel shows an error rather than "no matching variants". An error means the lookup failed, not that the variant is absent from that source. ## ClinVar Shows what ClinVar knows about this variant or region — the clinical assertions others have submitted. * **Clinical significance** — Pathogenic, Likely pathogenic, VUS (variant of uncertain significance), Likely benign, Benign, Conflicting, or Not provided, shown as a color-coded badge. * **Summary counts** — how many overlapping ClinVar records fall into each significance category, so you can see the balance of evidence at a glance. * **Condition** — the associated disease or phenotype. * **Review status** — ClinVar's confidence, shown as a 0–4 star rating. * **Overlap** — for region-based matches (e.g. structural variants), the reciprocal overlap between your variant and the ClinVar record, as a percentage. * **Link** — opens the variant's ClinVar entry. ## gnomAD Shows how common the variant is in the general population — one of the most informative filters for ruling variants in or out. * **Allele frequency** — the population frequency, with a rarity badge: **Very rare** (< 0.01%), **Rare** (0.01–1%), or **Common** (> 1%). * **Allele count/number** — the raw observed counts behind the frequency. * **Consequence** — the major predicted functional consequence. * **Filters** — the gnomAD quality filters on the record (e.g. `PASS`). * **Structural variants** — additionally show SV type and length, plus the reciprocal overlap with the matched gnomAD SV. * **Link** — opens the variant in the gnomAD browser. ## HiFi Solves Shows the variant's frequency within the HiFi Solves reference cohort — an internal long-read population that complements gnomAD, especially in regions long-read data resolves better. * **Cohort frequency** — allele count, total alleles, and allele frequency. * **Genotype breakdown** — homozygous, heterozygous, and hemizygous counts. * **Sample count** and the **collections** the variant was observed in. * **Overlap** — reciprocal overlap for region-based matches. * **Variant ID** — the cohort's identifier for the matched variant. {% hint style="info" %} **Reading frequency for interpretation.** A high population frequency in gnomAD or HiFi Solves argues against pathogenicity; absence or extreme rarity keeps a variant in contention. Use these panels together — a variant rare in gnomAD but common in HiFi Solves may simply be better ascertained by long reads. {% endhint %} ## The Gene tab The variant drawer's **Gene** tab describes each gene the variant affects. Expand a gene card to see: * **Location** and **NCBI Gene ID**. * **PLI Score** and **LOEUF Score** — gnomAD's measures of how intolerant the gene is to loss of function, with a link to gnomAD. * A gene summary and its aliases. * **Transcripts (RefSeq)**. * **Other variants in \** — see below. ### Other variants in the gene Under the transcripts, **Other variants in \** lists the case's other variants in that gene, of every type, with the total count in the heading. It helps you spot a second hit, such as a structural variant or repeat expansion in the same gene as a small variant. Each row shows: * a type chip (**SNV**, **SV**, **CNV**, **TR**, **PARA**, **METH**), coloured by classification. Your classification is used where you've made one, otherwise the automated one. Hover the chip for the full classification; * an **HFS** badge with the HiFi Solves allele frequency, where available; * how the variant relates to the gene: **in gene** (annotated to it), **overlaps** (within the gene, ±2 kb), **gene family** (a variant in a paralogous gene), or **overlapping region** (a methylation region); * the coordinate and a one-line summary. Rows are ordered from most to least severe classification, with unclassified variants last. The first five are shown, followed by a count of the rest. To see them all, search for the gene on the [Search tab](/products/workbench/variant-interpreter/reviewing-variants/search.md). {% hint style="info" %} If one variant type couldn't be searched, the list says so. Other variants of that type may still exist in the gene. {% endhint %} --- # Agent Instructions This documentation is published with GitBook. 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