> 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/small-variants.md). # Small variants (SNVs & indels) Small variants are single-nucleotide variants (SNVs) and short insertions or deletions (indels). In long-read WGS they are called per-sample, joint-called across a family where applicable, and phased so that you can see which variants sit on the same chromosome copy. ## The candidate table Each row is one 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 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 variant is located. | | **Pos** | The genomic coordinate (position) of the variant. | | **REF** | The reference allele at the variant position. | | **ALT** | The alternative allele observed. | | **Gene Symbol** | The standard HGNC gene symbol of the affected gene. | | **Max AF** | The maximum allele frequency observed for the variant across any sub-populations in reference datasets. | | **1000G AF** | The allele frequency of the variant in the 1000 Genomes Project cohort. | | **gnomAD Exome AF** | The allele frequency of the variant in the gnomAD exomes database. | | **gnomAD Genome AF** | The allele frequency of the variant in the gnomAD genomes database. | | **Biotype** | The biological classification of the transcript (e.g., `protein_coding`, `lncRNA`). | | **Consequence** | The predicted functional effect of the variant on the transcript (e.g., `missense_variant`, `frameshift_variant`). | | **Impact** | The predicted severity impact of the variant's consequence (e.g., `HIGH`, `MODERATE`, `LOW`, `MODIFIER`). | | **Phenotype Association** | Known clinical phenotypes, traits, or diseases associated with the gene. | | **Variant Class** | The structural classification of the variant (e.g., `SNV`, `Insertion`, `Deletion`). | | **Exomiser Rank** | The gene ranking generated by Exomiser based on phenotype relevance and variant pathogenicity. | | **Exomiser Inheritance** | The predicted mode of inheritance for the disease matching the phenotypes. | | **Exomiser Variant Score** | The score computed by Exomiser assessing the potential pathogenicity of the variant. | | **Exomiser Functional Class** | The functional consequence class predicted by Exomiser. | | **Exomiser ACMG Classification** | The pathogenicity classification assigned by Exomiser following ACMG guidelines. | | **Exomiser ACMG Disease** | The specific disease associated with the gene that matches the patient's phenotypes according to Exomiser. | | **Genotype** | The zygosity and phase of the variant in the sample. | ## Filters The filter drawer offers: * **User Classification**: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign. * **Gene**: filter by gene symbol. * **Chromosome**: chr1 to chr22, chrX, chrY. * **Position**: a genomic-coordinate range. ## How to review 1. Sort or filter the table to bring the most relevant candidates to the top, typically rare, predicted-damaging variants in phenotype-relevant genes. 2. Select a variant to open its detail view, where you can inspect the supporting reads and annotations. 3. Record a decision (e.g. include, exclude, follow up) so it carries into the [report](/products/workbench/variant-interpreter/generating-a-report.md). {% hint style="info" %} Phasing matters for recessive conditions. When two heterozygous variants fall in the same gene, phasing tells you whether they are on the same copy (likely benign together) or on opposite copies (a potential compound heterozygote). See the phasing background on the [Paralogs](/products/workbench/variant-interpreter/reviewing-variants/paralogs.md) page. {% 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. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/small-variants.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. 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