> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info.md).

# Variant info

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

{% hint style="info" %}
Variant types **TRA** (translocation), **INV** (inversion), and **BND** (breakend) are supported from v100.41.0+.
{% endhint %}

## Details included

* **Variant type**
* **Main effect**
  * TRA, INV: The most severe effect across the participating breakpoints.
  * TRA, INV — Main Effect BP1: Main effect at breakpoint 1.
  * TRA, INV — Mate Effect BP2: Main effect at breakpoint 2.
* **Cytoband** (unavailable for TRA, INV, and BND in v100.41)
* **Phasing (v100.40+, 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(s)**
* [**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
  * **TRA, INV:**
    * **Transcript of gene 1**
    * **Transcript of gene 2**
* **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 behaviour 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)**
* [**Resources**](/emedgene/emedgene-analyze-manual/variant_page/clinical_significance_section/variant-info/resources.md): Links to external databases with pre-filled search queries
  * **TRA, INV:** Resources per breakpoint
* **SV type (DEL, DUP, INS, TRA, INV, BND)**
* **SV Length (DEL, DUP, INS, INV)**
* **DECIPHER link (DEL, DUP, INS)**
* **ISCN notation (DEL, DUP, INS)**
* **Inverted genes (INV)**
* **ALT (INV, TRA, BND)**: `ALT` field from the VCF
* **Mate BND:**
  * **INV, TRA**: Link to the mate BND
  * **BND**: Link to the mate INV or TRA variant

### MRJD region group and copy fields (v100.41.0+)

These fields apply to variants from **MRJD (Multi Region Joint Detection)** analysis. They show which MRJD region group a variant belongs to and which copy assignment(s) within that group apply to the call. That copy context is what links variants in Connected variants (connection type Hap) and supports copy granularity filtering for MRJD haplotype and CNV reviews.

{% hint style="info" %}
**Note:** This is not the same as pharmacogenomic (star-allele) haplotype naming. Star-allele/PGx haplotype identifiers are documented separately for PGx haplotype variants.
{% endhint %}

* **MRJD haplotype variants**
  * Haplotype name: Label for the MRJD haplotype call (when shown).
  * Copy:X|Y (under Haplotype name, when available): Which copy assignment(s) in the MRJD region group this haplotype is associated with (for example, that copies 1 and 2 belong to this haplotype). Values are shown as reported from the MRJD call; use them with Region Group Name and Connected variants to see related SNV/CNV calls on the same copy assignment.
  * Individual genotype: Shown only when a value is available; hidden when empty.
* **SNV/indel (MRJD cases)**
  * Region Group Name (under Type, when available): MRJD region group that groups this variant with related MRJD haplotype and CNV calls in the case.
  * Copy:X|Y (under Region Group Name, when available): Which copy assignment within that region group this variant is placed on (for example, that the SNV lies on copy 4). Used with Connected variants to find haplotype/CNV calls that share the same region group and copy assignment.
* **CNV (DEL, DUP, INS in MRJD cases)**
  * Region Group Name (under Type, when available): MRJD region group shared with related haplotype and SNV/indel calls.
  * Region Name (under Region Group Name, when available): Named region within that group.
  * Copy (under Region Name, when available): Copy assignment for this CNV within the region group (which copy index the CNV call is associated with), not a generic “CNV size” field. Use with Connected variants and advanced copy granularity filters when reviewing MRJD CNVs.

## 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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