> 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 tab opens pre-filtered to an **Automated Classification** of Pathogenic or Likely Pathogenic, sorted with the most severe classification first. This matches the small-variant count on the [Summary tab](/products/workbench/variant-interpreter/getting-started/the-summary-tab.md). Clear the filter to see every small variant.

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.
* **Automated Classification**: the pipeline's ACMG classification, taken from Exomiser. This tab opens pre-filtered to Pathogenic and Likely Pathogenic.
* **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. The **Evidence in this sample** card shows the allele depth and variant allele fraction behind the call.
3. If another small variant falls in the same gene, check the **Haplotype phase** panel at the top of the detail view to see whether the two are in cis or in trans. See [Haplotype phase (cis/trans)](/products/workbench/variant-interpreter/reviewing-variants/haplotype-phase.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" %}
Phasing matters for recessive conditions. When two heterozygous variants fall in the same gene, phasing tells you whether they are on the same haplotype (**in cis**, so one copy of the gene may still be intact) or on opposite haplotypes (**in trans**, a potential compound heterozygote). See [Haplotype phase (cis/trans)](/products/workbench/variant-interpreter/reviewing-variants/haplotype-phase.md).
{% 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 by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/small-variants.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.