# Manually add variants to a delivered case
In some cases, you may need to record variants that were not included in the uploaded VCF or not called from FASTQ data. This is particularly useful when:
* You are complementing NGS results with findings from other genetic tests (e.g., long-read sequencing, optical mapping, CGH, SNP array, karyotyping/FISH, repeat-primed PCR, MLPA, Southern blot, etc.)
* You wish to report on adjacent CNV calls as a single CNV event.
* You wish to report a set of adjacent variants together as a single multi-nucleotide variant (MNV).
Manually adding variants ensures that all relevant findings are visible in the case review and can be considered during interpretation.
Currently supported variant types: **SNV, CNV, UPD, ROH, and STR**.
{% hint style="info" %}
**Note:** SV support is planned for future releases.
{% endhint %}
***
## To manually add a variant:
1. Open the **Analysis Tools** tab.
2. Click the **plus (+) button** in the top-right corner.
{% hint style="info" %}
**Note:** If you do not see the option, please contact support to verify your user role permissions.
{% endhint %}
3. In the **Manually Add Variant** window, select the variant type: SNV, CNV, UPD, ROH, or STR.
4. Fill in the details based on the selected type:
{% tabs %}
{% tab title="SNV or ROH" %}
* Chromosome,
* Position,
* REF,
* ALT,
* Zygosity
{% endtab %}
{% tab title="CNV or UPD" %}
* Chromosome,
* Position Start,
* Position End,
* REF,
* ALT,
* Type:
* CNV: DEL, DUP,
* UPD: IUPDMAT (maternal isodisomy), IUPDPAT (paternal isodisomy), HUPDPAT (paternal heterodisomy), HUPDMAT (maternal heterodisomy),
* Zygosity
{% endtab %}
{% tab title="STR" %}
* Chromosome,
* Position,
* REF Repeats Number,
* ALT Repeats Number,
* Repeats Unit,
* Zygosity
{% endtab %}
{% endtabs %}
5. Click on **Create Variant** to add it to the case.
## Viewing manually added variants
* Manually added variants have a **blue frame** and are clearly marked with the label *“Manually added variant”* on the Variant page.
* These variants differ from pipeline-called variants:
* **Quality** and **Visualization** sections are not available.
* **Population Statistics** are not shown.
* **Automatic ACMG scoring** is not applied, but you can still manually add ACMG tags, interpretation notes, and classifications.
## Sorting and formatting notes
* STR variants that are added manually do not fully align with the pipeline-called STR format. For example, variant length is not displayed.
* Manually added variants cannot be sorted by columns that do not apply, such as **AI Rank**.
{% hint style="success" %}
**Tip:** When reviewing manually added STRs, rely on the repeat numbers and unit provided, since length formatting is not included.
{% endhint %}
## Filtering manually added variants
To view only the variants you have added manually:
* In the **Evidence & Tags Filters** section, select **Manually added variants**.
This helps you focus specifically on variants that were entered outside of the automated pipeline.
%20(1).png?alt=media)
.png?alt=media)
.png?alt=media)