# Was the silent mutation removed from the OmicsSomaticMutations.csv in 24Q2?

**URL:** <https://forum.depmap.org/t/was-the-silent-mutation-removed-from-the-omicssomaticmutations-csv-in-24q2/3368>\
**Category:** Q&A\
**Created:** [June 25, 2024, 7:29am UTC](https://forum.depmap.org/t/was-the-silent-mutation-removed-from-the-omicssomaticmutations-csv-in-24q2/3368 "2024-06-25T07:29:20Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![SongSong](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@SongSong](https://forum.depmap.org/u/SongSong)\
**Post date:** [June 25, 2024, 7:29am UTC](https://forum.depmap.org/t/was-the-silent-mutation-removed-from-the-omicssomaticmutations-csv-in-24q2/3368/1 "2024-06-25T07:29:20Z")

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Hi, Sorry for the frequent question.  
While checking the 24Q2 dataset, I found that there were no silent mutation labels in the OmicsSomaticMutation.csv file.  
Although I filtered out the silent mutations from the previous version of the dataset (i.e., 23Q2), were they removed automatically from the current version?

+) The number of genes in the OmicsCNGene.csv file was slightly reduced from 25368 to 24383 compared to the 23Q2 version of the same file. Can anyone explain about this?

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [June 25, 2024, 12:55pm UTC](https://forum.depmap.org/t/was-the-silent-mutation-removed-from-the-omicssomaticmutations-csv-in-24q2/3368/2 "2024-06-25T12:55:48Z")

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Hi,

To your first question, yes, we had a major pipeline update in 23Q4 and removed all of the silent mutations, among others. Please refer to our [documentation](https://storage.googleapis.com/shared-portal-files/Tools/24Q2_Mutation_Pipeline_Documentation.pdf) on the mutation pipeline for more details.

To your second question, in 23Q4 we started masking genes that fall in segmentally duplicated/short repeat regions in our copy number matrix. [This section](https://forum.depmap.org/t/announcing-the-23q4-release/2929#copy-number-and-mutation-known-segmental-duplication-regions-10) of our 23Q4 release announcement describes this change.

Thanks,  
Simone