> 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/structural-variants.md). # Structural variants Structural variants (SVs) are larger rearrangements, deletions, insertions, duplications, inversions, and translocations, typically ≥ 50 bp. Long-read sequencing resolves many SVs that short reads miss, especially in repetitive regions. Copy-number variants are reviewed on their own tab; see [Copy number](/products/workbench/variant-interpreter/reviewing-variants/copy-number.md). ## Visualizations The Structural Variants tab adds visualizations to make review easier. Switch between them with the toggle in the upper-right of the toolbar: * **Track** (default): the variants laid out along each chromosome, colour-coded by type, with a length histogram. * **Circos**: the genome as a ring, with chords linking each SV's two breakpoints. A **Type** dropdown in the same toolbar filters the table and chart to one SV type. ### The Circos plot Each chord joins the two breakpoints of a structural variant and is coloured by the chromosome it starts on. The plot shows: * every translocation (BND). The two records describing either end of the same translocation are drawn as one chord; * large same-chromosome events (deletions, duplications, inversions) spanning 250 kb or more. When there are too many to draw clearly, the plot shows the inter-chromosomal links first, then the longest-range ones, and the caption under the plot tells you it's showing only part of the set. To use the plot: 1. Hover a chord to highlight it. The tooltip shows both breakpoints, the SV type and span, and the genes involved. 2. Click a chord to filter the table to that SV type. 3. Click the expand button (above the zoom controls) to let the plot fill the content area. Click it again to bring back the variant list. {% hint style="info" %} The Circos plot follows the table's active filters. Because this tab opens pre-filtered to an Automated Classification of Pathogenic and Likely Pathogenic, the chords initially show only those variants. Clear the filter to see the links for every SV. {% endhint %} ## The candidate list Alongside the visualizations, the variant list shows the SV calls. 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 structural 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. | | **Chrom** | The chromosome where the structural variant is located. | | **Pos** | The starting genomic coordinate (position) of the structural variant. | | **SV Type** | The type of structural variant (e.g., `DEL` (deletion), `INS` (insertion), `DUP` (duplication), `INV` (inversion), `BND` (breakend/translocation)). | | **SV Length** | The length of the structural variant in base pairs. | | **Genes** | Standard gene symbols of the genes overlapped or affected by the structural variant. | | **HiFi Solves AF** | The allele frequency of the structural variant in the HiFi Solves reference database. | | **gnomAD Allele Frequency** | The allele frequency of the structural variant in the gnomAD SV database. | | **Pathogenicity Score** | A composite pathogenicity score calculated for the structural variant. | | **Exomiser Score** | The score computed by Exomiser assessing the potential pathogenicity and phenotypic relevance of the variant. | | **PhenoGenius** | The pathogenicity score computed by PhenoGenius based on phenotypic relevance and genomic annotations. | | **AnnotSV Score** | The annotation/pathogenicity score or class assigned by AnnotSV. | | **StrVCTVRE Score** | The score computed by StrVCTVRE, assessing pathogenicity of structural variants affecting exons. | | **Genotype** | The zygosity and phase of the structural variant in the sample. | Where an SV overlaps several genes, gene-level scores such as **PhenoGenius** show the highest value across those genes. Selecting a variant opens its detail view. It explains why the call was made, shows the reads that support it, and gathers the clinical, population, and predicted-effect evidence. See [Structural variant detail](/products/workbench/variant-interpreter/reviewing-variants/structural-variants/structural-variant-detail.md). ## 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. * **Gene**: filter by gene symbol. * **SV Type**: DEL, INS, DUP, BND, INV. * **Chromosome**: chr1 to chr22, chrX, chrY. * **Position**: a genomic-coordinate range. ## How to review 1. Use the **Track** and **Circos** views to orient on the events and their genomic context. 2. Focus on rare events overlapping phenotype-relevant genes. 3. For each candidate, open the detail view and review type, size, overlapping genes, and read support. See [Structural variant detail](/products/workbench/variant-interpreter/reviewing-variants/structural-variants/structural-variant-detail.md). 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). {% hint style="info" %} SVs are evaluated by which genes and regions they overlap, not by a single position. Two events of the same type can differ greatly in significance depending on exactly which exons they intersect. {% endhint %} --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. 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