> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.illumina.com/emedgene/release-notes/change_log/change_log_pipeline_31.md).

# Change log pipeline 31

## Features

* Pipeline version naming changed to match workbench version.
* Annotation | Ensembl Variant Effect Predictor (VEP) updated to version 108
  * Refseq transcripts updated to version [110](https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/110/)
  * The following effect modifications are updated in Filters > Severity > Simple mode
    * New effect types: splice\_donor\_5th\_base\_variant, splice\_donor\_region\_variant, splice\_polypyrimidine\_tract\_variant, start\_lost, start\_retained\_variant
    * Modified effect types:
      * nc\_transcript\_variant ==> non\_coding\_transcript\_variant
      * nmd\_transcript\_variant ==> NMD\_transcript\_variant
      * non\_coding\_exon\_variant ==> non\_coding\_transcript\_exon\_variant
    * High severity CNV duplication calculation was expanded to include splice\_polypyrimidine\_tract\_variant\_, coding\_sequence\_variant & intron\_variant&\_feature\_elongation in the severity calculation
* Added support for [DRAGEN *Expansion Hunter's*](https://github.com/illumina-swi/emedgene-docs/blob/prod/docs/q_and_a/how_do_i_prepare_vcf_files_generated_by_dragen_str_\(expansionhunter\)_to_be_used_as_input_for_emedgene.md) latest default catalog of 60 pathogenic STR loci (including 30 from gnomAD).
* Added support for DRAGEN 4.0 for VCF cases (with disabled Machine Learning pipeline).
* Labs running small panels can define gene list threshold below which case will deliver even without *AI Shortlist* results.

## Bug Fixes

* *AI Shortlist* | In a previous version, the algorithm for defining compound heterozygous variants was broken for pedigrees with additional samples. There is now support for compound heterozygous variants in any pedigree in the *Autosomal Recessive - Compound Heterozygotes* [*Inheritance Filter*](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/inheritance_filters.md) and *Auto Analysis* [*User Filter*](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/simple-filter-operators-mode/user_filters.md).
* ACMG Automation | SNVs | Automatic PM5 ACMG tag calculation for SNVs is now more precise.
* Annotation | REVEL | Updated REVEL scores with GRCh38 positions.
* Annotation | mtDNA | APOGEE and MitoTIP mtDNA variant missense prediction scores are displayed again.
* Annotation | ClinGen | Consistent annotation for CNVs classified as Uncertain by ClinGen in GRCh38 cases.
* Variant Page | Format of dbSNP link is fixed.
* Population Statistics | Fixed the issue with CNV population data being displayed incorrectly in some cases.


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