# Variant info

The **Variant info card** provides key details about the variant.

## Details included

* **Variant type**
* **Main effect**
* **Cytoband**
* **Phasing** (v100.40.0+, DRAGEN 4.5+, TruPath Genome data, SNVs/MNVs/indels):
  * Phase block identifier
  * Phased genotype (if available): [`A`](#user-content-fn-1)[^1], [`B`](#user-content-fn-2)[^2], [`AB`](#user-content-fn-3)[^3]
* **Zygosity** for each sequenced family member
* **Gene symbol**
* [**Transcript**](/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/transcript.md): Variant description in HGVS[^4] nomenclature, based on the selected transcript
* **Exon information**: Exon number and total number of exons for the selected transcript

{% hint style="warning" %}
**Note**: For some variants, exon information may be shown as `-/-`.

This is expected behavior when exon numbering is not applicable, such as for variants that span the entire transcript (for example, whole-gene or whole-transcript variants), intronic variants, or variants located outside the transcript.
{% endhint %}

* **dbSNP ID** (SNV/indel only)
* [**Resources**](/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/resources.md): 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

## **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. This streamlines interpretation and reduces manual sorting 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 could not 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 the *CYP21A2* and *GBA* callers enabled.

### **Repeat**

### **Suspected MNP**

[^1]: Genotype `1|0`

[^2]: Genotype `0|1`

[^3]: Genotype `1|1`

[^4]: Human Genome Variation Society


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