> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant_page/connected-variants-tab.md).

# Connected variants tab

The **Connected variants tab** 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:** SNV, indel, MNV (v100.39 and later), DEL, DUP, INS, mtDNA SNV/indel, STR, and MRJD haplotype (v100.41 and later).

{% hint style="info" %}
This feature is not available for star allele haplotypes, manually added variants, LOH/ROH, translocations (TRA), inversions (INV), and breakend (BND) variants.
{% endhint %}

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, Hap (v100.41 and later). Two variants may share more than one connection type.
* **Phasing**: Phase block identifier and phased genotype, when available.
* **Known Variants** (v100.41 and later): Color-coded badges for variant's pathogenicity in public or private variant databases.

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.

{% hint style="info" %}
Only the **first 50 connected variants** are displayed.
{% endhint %}

## Variant connection types

### MNV (Multi-nucleotide variant)

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

### JIDS (Region-ambiguous variants)

Connection between [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](/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section.md).

### Compound heterozygote

Connection between two different variants in the same gene that are inherited from different parents.

### Hap (v100.41 and later)

Connection between variants from the same multi-region joint detection (MRJD) analysis.

Which variants are connected depends on the variant under review:

* **MRJD haplotype or MRJD CNV**: SNVs in the same or an overlapping region group and on the same copy, and other MRJD haplotypes and CNVs in the same region group.
* **SNV**: MRJD haplotypes and CNVs in the same or an overlapping region group and on the same copy.

## Modes

In the **Connected Variants tab**, you can choose between two modes. To switch modes, select **Switch to simple** or **Switch to advanced** above the table.

### Simple mode

**Simple mode** shows all connected variants without filters.

### Advanced mode

**Advanced mode** lets you narrow the table by:

* Connection type
* Specific copy (v100.41 and later)

#### Connection type filter

You can select one or more connection types: **MNV**, **JIDS**, **Compound heterozygote**, or **Hap** (v100.41 and later).

<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><p>Connection type filter on the <strong>Connected Variants tab</strong>.</p></figcaption></figure>

#### Copy filter (v100.41 and later)

When you review an MRJD haplotype or an MRJD CNV, you can select only the variants on a specific copy of the region group. By default, the table shows variants from all copies.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-92101d94977a571935bf2dc8d0f645ca2f207c95%2F41_connected_variants_copy_filter.gif?alt=media" alt=""><figcaption><p>Copy filter on the <strong>Connected Variants tab</strong>.</p></figcaption></figure>

[^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.


---

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