> 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-curate-manual/curate-articles/curate-article-page/linked-variants.md).

# Variant card

## Card contents

The **Variant** **card** on the [**Curate Article page**](/emedgene/emedgene-curate-manual/curate-articles/curate-article-page.md) lists variants associated with the article.

Each linked variant shows:

* Associated genes. For a CNV, up to three genes are shown; hover to view the remaining genes.
* HGVS notation, or variant details when HGVS notation is unavailable.
* Pathogenicity.

Variant details use the human reference selected in **Curate**. When a linked variant is associated with a **Curate** variant, select its card to open the [**Curate Variant page**](/emedgene/emedgene-curate-manual/curate_variants/curate_variant_page.md).

[Adding](#how-to-add-a-variant-to-an-article) and [deleting](#how-to-delete-a-linked-variant) linked variants, and [updating pathogenicity](#how-to-update-the-pathogenicity-of-a-linked-variant) require the appropriate [user roles](/emedgene/emedgene-analyze-manual/settings/user_roles.md).

***

## How to add a variant to an article

{% hint style="warning" %}
**Curate** does not allow a variant that is already linked to the article to be added again.
{% endhint %}

{% stepper %}
{% step %}
In the article's **Variant card**, select **Add**.
{% endstep %}

{% step %}
Select the human genome reference (GRCh37 or GRCh38).
{% endstep %}

{% step %}
Select the variant type:

* **SNV**: Single nucleotide variant or indel variant
* **CNV:** Deletion or duplication
  {% endstep %}

{% step %}
Enter variant details.

**SNV variant details**

Enter variant details using genomic coordinates or an HGVS coding change.

* **Genomic position nomenclature**

| Field name   | Expected input                                   | Example  |
| ------------ | ------------------------------------------------ | -------- |
| `Chromosome` | `1` - `22`, `X`, `Y`, `M`                        | `X`      |
| `Position`   | Integer                                          | `123000` |
| `REF`        | `A`, `T`, `G`, `C`, or a string of these letters | `G`      |
| `ALT`        | `A`, `T`, `G`, `C`, or a string of these letters | `GACT`   |

* **Coding change nomenclature**

| Field name   | Expected input                                                                                                                                                    | Example                                                                                                                           |
| ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
| `Gene`       | Search by gene symbol, NCBI ID, or HGNC ID                                                                                                                        | `SMN1`                                                                                                                            |
| `Transcript` | <p>Select from the options.<br>If a preferred transcript is set on the gene’s <strong>Curate</strong> page, it is selected by default and marked with a star.</p> | `NM_000344.4`                                                                                                                     |
| `c.dot`      | Coding change                                                                                                                                                     | <p>SNV: <code>c.403G>T</code><br>Small insertion: <code>c. 4713\_4714insTA</code><br>Small deletion: <code>c.65\_66del</code></p> |

**CNV variant details**

| Field name       | Expected input                                   | Example  |
| ---------------- | ------------------------------------------------ | -------- |
| `Chromosome`     | `1` - `22`, `X`, `Y`, `M`                        | `14`     |
| `Position start` | Integer                                          | `123000` |
| `Position end`   | Integer. Must be greater than `Position start`.  | `124000` |
| `REF`            | `A`, `T`, `G`, `C`, or a string of these letters | `G`      |
| `Type`           | `DEL`, `DUP`                                     | `DEL`    |
| {% endstep %}    |                                                  |          |

{% step %}
Select **Pathogenicity**.
{% endstep %}

{% step %}
Select **Add**.
{% endstep %}
{% endstepper %}

**Result:**

* The variant is linked to the article.
* If a record for the variant exists in **Curate Variants**: A link to the **Curate** variant page (<i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i>) appears instead of **Add variant to Curate** (<i class="fa-circle-plus">:circle-plus:</i>).
* **Curate** records an [activity](/emedgene/emedgene-curate-manual/curate-articles/curate-article-page/activities-panel.md).

***

## How to add a linked variant to Curate

On the linked variant, select **Add variant to Curate** (<i class="fa-circle-plus">:circle-plus:</i>).

**Result:**

* **Curate** creates a matching **Curate** variant or associates an existing Curate variant entry with the linked variant for the article.
* A link to the **Curate** variant page (<i class="fa-arrow-up-right-from-square">:arrow-up-right-from-square:</i>) appears instead of **Add variant to Curate** (<i class="fa-circle-plus">:circle-plus:</i>).

{% hint style="warning" %}
The linked variant and its corresponding **Curate** variant maintain independent pathogenicity values. Updating one does not update the other.
{% endhint %}

***

## How to update the pathogenicity of a linked variant

{% stepper %}
{% step %}
On the linked variant, select **Edit** (<i class="fa-pen">:pen:</i>).
{% endstep %}

{% step %}
Select a different pathogenicity from the dropdown.
{% endstep %}

{% step %}
Select **Save**.
{% endstep %}
{% endstepper %}

**Result:**

* The pathogenicity of the linked variant is updated
* **Curate** records the previous and updated values in an [activity](/emedgene/emedgene-curate-manual/curate-articles/curate-article-page/activities-panel.md).

***

## How to delete a linked variant

{% stepper %}
{% step %}
On the linked variant, select **Delete** (<i class="fa-trash-can">:trash-can:</i>).
{% endstep %}

{% step %}
Select **Delete** in the dialog window to confirm.
{% endstep %}
{% endstepper %}

**Result:** The association is removed from the article. The corresponding **Curate** variant is not deleted.


---

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