> 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: * **Track & histogram view**: the variants laid out along the genome, colour-coded by type. * **Circos plot**: shows the relationships between variants across the genome (for example, the two ends of a translocation). ## 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. | Selecting a variant opens its detail view, where you can inspect the call, explore the affected gene, open **IGV**, and **classify** the variant to add it to the report. ## 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/histogram 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, review type, size, and overlapping genes in the detail view. 4. Classify and add findings to 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. 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