Clinical significance tab

The Clinical Significance tab provides essential variant-level and gene-level details to help you evaluate a variant’s potential pathogenicity. It combines AI-driven insights with curated public data for informed interpretation.

Information is organized into the following cards:

• Variant info: Displays key details such as HGVS nomenclature, predicted effect, variant type, zygosity, and links to external databases.

• In silico predictions: Shows individual tool results and algorithmic predictions for missense, conservation, and splicing effects.

• Gene metrics: Summarizes gene’s level of intolerance to different types of variation.

• Clinical significance: Highlights previous pathogenicity classifications from your lab and public sources.

• Gene-related diseases: Lists known gene–disease associations with inheritance patterns and source links.

Variant badges

DRAGEN pipelines automatically assign variant badges to highlight specific call characteristics.

Integrating these badge filters into custom filter presets allows users to quickly identify variants that may need further review or validation, streamlining interpretation and minimizing manual sorting efforts by grouping similar variants together.

Ambiguous Calling

• Labels potential de novo germline small variants in paralogous segmental duplication regions of the genome.

• Requires DRAGEN 4.3+ MRJD caller in High Sensitivity Mode (enabled by default when running DRAGEN through Emedgene).

Homology Region

• Labels small variants located in regions of high sequence similarity, reflecting potential mapping ambiguity due to paralogous sequences.

• Requires DRAGEN 4.3+ Small variant caller in High Sensitivity Mode (enabled by default when running DRAGEN through Emedgene).

Imprecise

• Labels structural variants for which the exact breakpoints couldn't be confidently determined.

• Requires DRAGEN v4.4+ Structural variant caller.

Potential Mosaic

• Labels potential mosaic small variants.

• Requires DRAGEN 4.3+ Small variant caller in Mosaic Detection Mode (enabled by default when running DRAGEN through Emedgene with an allele frequency threshold of 0.2).

Recombinant

• Identifies variants that may reflect recombination‑type sequence exchange between a gene and its highly similar pseudogene:

  • When the exchange is reciprocal, it can produce a gene deletion or duplication.

  • When the exchange is non‑reciprocal, it results in a gene conversion, where a segment of pseudogene sequence replaces the corresponding part of the functional gene.

• Applicable only to variants in the GBA1/GBAP1 and CYP21A2/CYP21A1P genes.

• Requires DRAGEN 4.3+ Targeted caller with enabled CYP21A2 and GBA callers.

Repeat

Suspected MNP