# 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**](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info): Displays key details such as HGVS nomenclature, predicted effect, variant type, zygosity, and links to external databases.
* [**In silico predictions**](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/in-silico-predictions): Shows individual tool results and algorithmic predictions for missense, conservation, and splicing effects.
* [**Gene metrics**](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-metrics): Summarizes gene’s level of intolerance to different types of variation.
* [**Clinical significance**](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/clinical-significance): Highlights previous pathogenicity classifications from your lab and public sources.
* [**Gene-related diseases**](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/gene-related-diseases): Lists known gene–disease associations with inheritance patterns and source links.

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## **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](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection) in [High Sensitivity Mode](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection#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](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling) 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](https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline/sv-calling).

### **Potential Mosaic**

* Labels potential mosaic small variants.
* Requires DRAGEN 4.3+ [Small variant caller](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling) in [Mosaic Detection Mode](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/mosaic-detection) (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](https://help.dragen.illumina.com/dragen-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/targeted-caller) with enabled *CYP21A2* and *GBA* callers.

### **Repeat**

### **Suspected MNP**