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.

Note: This feature is not available for manually added variants.

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 link-out icon opens the variant in a new browser tab.

Only the first 50 connected variants are displayed.

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.

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, called by DRAGEN MRJD 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.

Tip: Use Calling Methodology filters to quickly isolate region-ambiguous variants for review.

Compound heterozygote

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