# Remove Background Mutations

The Remove background mutations task is a variants filtering task that enables you to filter variants against built-in databases, to clean up noise from common polymorphisms and benign mutations. The available built-in databases are:

* **Primate AI** \[1]: Prediction of pathogenicity on missense mutations. Percentile score ranges from 0 to 1, with 0 being benign, 1 being most pathogenic. *Global percentile* is based on global ranking of all missense variants in the human genome, while *Percentile* is based on ranking of all missense variants within the same gene.
* **Promoter AI** \[2]: Prediction of expression-altering consequences of variants at promoter regions. *Scores* range from -1 to 1. Positive score indicates variant likely enhances transcription, negative score indicates variant likely repress transcription.
* **gnomAD** \[3]: The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. Filtering by *minor allele frequency (MAF)* is supported.
* **DRAGEN Haplotype Database**: Proprietary haplotype database built from a panel of 256 population haplotypes. Filtering by *minor allele frequency (MAF)* is supported.

{% hint style="warning" %}
The databases in the Remove background mutations task support only human hg38 assembly.
{% endhint %}

## Running Remove background mutations

The Remove background mutations can be invoked from a Variants data node:

* Click to select a **Variants** data node.
* Select **Variant analysis** from context-sensitive menu, select **Remove background mutations.**
* Select a **database** for filtering, click **Next**.

<figure><img src="/files/6rJcJSYvOBm8YLtAhXQ9" alt="" width="527"><figcaption></figcaption></figure>

* Set **filtering criteria**, then click **Finish**.

<figure><img src="/files/hKAexRHrQ4Q4p43XC9OI" alt=""><figcaption></figcaption></figure>

If you need to filter variants on more than one databases, run the **Remove background mutations** tasks sequentially.

## References

1. Hong Gao et al. ,The landscape of tolerated genetic variation in humans and primates.Science380, eabn8153(2023). DOI:10.1126/science.abn8197
2. Kishore Jaganathan et al. ,Predicting expression-altering promoter mutations with deep learning. Science389, eads7373(2025). DOI:10.1126/science.ads7373
3. Karczewski, K.J., Francioli, L.C., Tiao, G. *et al.* The mutational constraint spectrum quantified from variation in 141,456 humans. *Nature* 581, 434–443 (2020). <https://doi.org/10.1038/s41586-020-2308-7>. <https://gnomad.broadinstitute.org/>


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