# Connected variants tab

The **Connected variants tab** introduced in v36.0 reveals connections between the variant under review and other variants in a case. This information can be crucial for assessing variant pathogenicity.

**Supported variant types:** SNVs, indels, MNVs, SVs, CNVs, mtDNA variants, and STRs.

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**Note:** This feature is not available for manually added variants.
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The number of connected variants appears in parentheses after the tab title (for example, "Connected Variants (3)").

## Connected variants table

For each connected variant, the table displays:

* **Variant details**: Gene name, variant type, genomic location, reference and alternate alleles, main effect, and dbSNP ID
* **Variant quality metrics (proband)**: Quality grade, sequencing depth, and allele bias
* **Zygosity** for the proband and parental samples, if available
* **Connection type(s):** MNV, JIDS, Compound heterozygote. Two variants may share more than one connection type

A <i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i> link-out icon opens the variant in a new browser tab.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-1a1a2d07bdbb77ebc0544a663579d5395b34ec89%2Fconnected%20variants%20link.gif?alt=media" alt=""><figcaption></figcaption></figure>

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Only the **first 50 connected variants** are displayed.
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## **Modes**

In the Connected Variants tab, you can choose between two modes:

* **Simple mode** shows all connected variants without filters
* **Advanced mode** lets you filter variants by specific relationship types for more focused analysis

To switch modes, **click the text link** ("Switch to simple" or "Switch to advanced") located above the table.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-3692f180ad98d5fa91ec9a7c0258e6cb34a244ba%2Fconnected%20variants.gif?alt=media" alt=""><figcaption></figcaption></figure>

## **Variant connection types**

**MNV (Multi-nucleotide variant)**

Variants occurring within 2 nucleotides that, if combined into one, may represent a multi-nucleotide variant.

**JIDS (Region-ambiguous variants)**

[Region-ambiguous variants](#user-content-fn-1)[^1], called by DRAGEN MRJD[^2] caller. These variants are linked together by a JIDS (Joined IDs) tag in the VCF INFO field containing positions of paralogous regions.

Emedgene marks these variants with an "Ambiguous calling" badge in the [Clinical significance tab](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section).

{% hint style="info" %}
Tip: Use [Calling Methodology filters](https://help.connected.illumina.com/emedgene/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/quality_filters#calling-methodology) to quickly isolate region-ambiguous variants for review.
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**Compound heterozygote**

A compound heterozygote occurs when two different variants in the same gene are inherited from different parents.

[^1]: Variants that could belong to more than one location in the genome.

[^2]: Multi Region Joint Detection. A method designed to detect de novo germline small variants in paralogous regions of the genome.