# Multiple Deletions

**URL:** <https://www.alphagenomecommunity.com/t/multiple-deletions/768>\
**Category:** Help & Support\
**Created:** [February 3, 2026, 1:19pm UTC](https://www.alphagenomecommunity.com/t/multiple-deletions/768 "2026-02-03T13:19:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ProximaCentauri](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/proximacentauri/32/725_2.png) [@ProximaCentauri](https://www.alphagenomecommunity.com/u/ProximaCentauri)\
**Post date:** [February 3, 2026, 1:19pm UTC](https://www.alphagenomecommunity.com/t/multiple-deletions/768/1 "2026-02-03T13:19:51Z")

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Hi there,

I was wondering if it is possible to use multiple deletions as input for a variant effect prediction simultaneously. I want to delete 6 different 20bp fragments at once and predict how this affects the genome around my gene of interest.

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**Author:** ![Tumi\_Makgatho](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/tumi_makgatho/32/703_2.png) [@Tumi\_Makgatho](https://www.alphagenomecommunity.com/u/Tumi_Makgatho)\
**Post date:** [February 6, 2026, 3:41pm UTC](https://www.alphagenomecommunity.com/t/multiple-deletions/768/2 "2026-02-06T15:41:28Z")

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Hi there,

Thank you for reaching out.

Currently, score\_variant is designed for single variants. You can try creating a single structured variant with all the deletions by defining the reference\_bases as the entire genomic span covering the sites and the alternate\_bases as that sequence with the fragments removed. Alternatively, manually construct the full DNA sequence string with all 6 fragments removed and input this custom sequence into the predict\_sequence() function,. You will then need to manually compare these predictions to those from the reference sequence to determine the combined effect.

Please also refer here for further assistance [Using AlphaGenome to predict the cooperativity of multiple SNPs?](https://www.alphagenomecommunity.com/t/using-alphagenome-to-predict-the-cooperativity-of-multiple-snps/530)

Kind regards,  
Tumi