> 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/copy-number.md). # Copy number Copy-number variants (CNVs) are changes in the number of copies of a region: losses (deletions) and gains (duplications). The Copy Number tab presents the CNV calls with visualizations built for dosage review. ## Visualizations Switch views with the toggle in the toolbar: * **Scatter**: a genome-wide view of the copy-number calls. * **Ideogram**: the calls arranged across the chromosomes. {% hint style="info" %} A **gene dosage matrix** is also part of this tab. It does not yet have a visualization; this page will be updated when it ships. {% endhint %} ### The ideogram Each call is drawn as a tick on its chromosome. The tick's width scales with the size of the event, so large events stand out. The legend shows how classification is marked: **Likely pathogenic** (outlined box), **Uncertain** (dot), and **Likely benign (no flag)**. Deletions and duplications are colour-coded. 1. Click a chromosome row to drill into that chromosome. The single-chromosome view shows its events against a megabase axis. 2. Click **Back** to return to the whole genome. 3. Click a tick to open that variant's detail view. ## Toolbar quick filters The toolbar above the chart offers quick filters that apply to both the chart and the table: | Control | What it does | | ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------ | | **Type** | Show one event type: **DEL**, **DUP**, or **LOH** (loss of heterozygosity). Each shows its count. | | **Classification** | Show calls by user classification: **Likely pathogenic** (Pathogenic and Likely Pathogenic), **Uncertain**, or **Likely benign** (Likely Benign and Benign). | | **Min size** | Hide events smaller than the chosen size: **≥ 50 kb**, **≥ 100 kb**, **≥ 200 kb**, **≥ 500 kb**, **≥ 1 Mb**, or **≥ 5 Mb**. | | **Other** | Show only calls that are not DEL, DUP, or LOH. It can't be combined with **Type**. | {% hint style="warning" %} The tab opens with **Min size** set to **≥ 50 kb**, so smaller events are hidden until you lower it. This applies to deletions and duplications alike. {% endhint %} ## The candidate table Each row is a genotyped copy-number variant. You can search, sort, filter, and customize the columns in the table using the **Columns** dropdown. The default columns in the candidate table include: | Column | Description | | ----------------------------- | --------------------------------------------------------------------------------------------------------------------------------- | | **User Classification** | The classification manually assigned to the copy-number variant by a reviewer (e.g., Pathogenic, Likely Pathogenic, VUS, Benign). | | **Automated Classification** | The automated classification generated by the system's pipeline rules or algorithms. | | **AnnotSV Score** | The pathogenicity annotation score or class assigned by AnnotSV. | | **SV Type** | The type of copy-number variant (e.g., `DEL` (deletion/loss), `DUP` (duplication/gain)). | | **Chrom** | The chromosome where the copy-number variant is located. | | **Pos** | The starting genomic coordinate of the copy-number variant. | | **End Position** | The ending genomic coordinate of the copy-number variant. | | **Genes** | Standard gene symbols of the genes overlapped or affected by the copy-number variant. | | **SV Length** | The length of the copy-number variant in base pairs. | | **Copy Number** | The copy-number genotype of the event. | | **Pathogenic Gain Phenotype** | The phenotype of known pathogenic gain regions the event overlaps. | | **Pathogenic Loss Phenotype** | The phenotype of known pathogenic loss regions the event overlaps. | | **Inheritance** | The parental origin of the event, where known. | | **ClinVar Significance** | The clinical significance of matching ClinVar records. | | **gnomAD Max AF** | The maximum allele frequency of matching gnomAD SVs. | | **Filter Status** | The filter status of the variant call from the caller (e.g., `PASS` or specific filtering flags). | ## Filters The filter drawer offers: * **User Classification**: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign. * **Automated Classification**: the pipeline's ACMG classification. This tab opens pre-filtered to Pathogenic and Likely Pathogenic. * **Type**: DEL (loss) or DUP (gain). * **Gene**: filter by gene symbol. * **Chromosome**: chr1 to chr22, chrX, chrY. * **Copy Number**: an integer copy-number range. * **Position**: a genomic-coordinate range. Event size is set with the **Min size** quick filter in the toolbar rather than in the drawer. ## How to review 1. Scan the scatter and ideogram views for calls flagged as likely pathogenic. Drill into a chromosome to see its events in detail. 2. Adjust **Min size**, **Type**, and **Classification** to focus the view. 3. Click a call to open its detail view and review the affected genes and dosage change (loss vs gain). 4. [Classify](/products/workbench/variant-interpreter/classifying-variants.md) the variant so it can be included in the [report](/products/workbench/variant-interpreter/generating-a-report.md). --- # Agent Instructions This documentation is published with GitBook. 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