Variant info

The Variant info card provides key details about the variant.

Details included

• Variant type

• Main effect

• Zygosity for each sequenced family member

• Gene symbol

• Transcript: Variant description according to the HGVS nomenclature based on the selected transcript

• Exon information: Exon number and total number of exons for the selected transcript

• dbSNP ID (SNV/Indel only)

• Resources: Links to external databases with pre-filled search queries

• CNV/SV-specific data:

  • SV Type (e.g., DEL, DUP)

  • SV Length

  • DECIPHER link

  • ISCN notation

  • Cytoband location

Variant badges

Variant badges are quick visual indicators that highlight special characteristics or potential interpretation challenges of a variant. They help identify variants that may require extra attention during review.

• Homology Region

  In Emedgene, variants located in regions of high sequence similarity are labeled with the Homology Region tag, reflecting potential mapping ambiguity due to paralogous sequences. This tag is automatically applied when High Sensitivity Mode is enabled (default), helping users identify variants that may require orthogonal validation. Users can also create preset filters using this tag to streamline variant triage in complex genomic regions.

• Potential Mosaic

  Emedgene now applies the Potential Mosaic tag to variants identified by its improved mosaic calling model, which delivers 4× fewer false positives than DRAGEN 4.2 High Sensitivity Mode and outperforms other mosaic callers in both speed and accuracy. Mosaic detection is enabled by default when running DRAGEN through Emedgene, with an allele frequency threshold of 0.2, and users can streamline interpretation by creating preset filters using this tag.

• Ambiguous Calling

  Emedgene now tags variants from segmental duplication regions with Ambiguous Calling, reflecting their uncertain placement due to poor mappability across ~5% of the genome. These variants are detected using the MRJD caller, which performs haplotype-based de novo small variant calling across paralogous regions, and are linked via a unique identifier (JIDS) in the new Connected Variants component. When DRAGEN is run through Emedgene, MRJD High Sensitivity Mode is enabled by default, and users can filter these variants using the Calling Methodology filter.

• Suspected MNP

• Repeat

• Recombinant