We are excited to announce that Franklin has been upgraded to use gnomAD version 4.1 for hg38 samples. This new version of gnomAD introduces significant improvements, as detailed in the gnomAD v4.1 blog.

With this update, Franklin now displays both exome, genome, and aggregated (joint) frequency data. However, please note that we have reverted to using the gene constraint data from version 2.1. This decision is based on a gnomAD blog post indicating that the v4 gene constraint data is still experimental.

We are also working towards adding a lifted-over version of gnomAD for hg19 cases in the near future. Stay tuned for more updates!

Franklin is introducing a new filtration display that will show your quick filters in a tree structure, making it easier to visualize your filters. This visualization will gradually roll out to all accounts over the next month. To view the tree display of the quick filter, click on the tree icon that appears when you hover over the quick filter box.

This visualization easily presents all of the filtration steps configured to the filter tree, and shows the number of variants that are protected in each filtration step.

At the first phase, this upgrade is available for germline cases and SNV’s and indels only.

As part of the filter tree improvements, Franklin now displays the quick filter labels that have kept each variant in their filtration. The labels are displayed in both tile or table variant views.

Alongside the tree visualization, this update will enhance the performance of the variants page, resulting in faster loading times for quick filter results.

The primary change introduced with this feature is that the calculation of filter results now occurs during the case's initial processing (variant annotation step at the time of case creation). This improvement allows Franklin to significantly reduce the time required to display filtered variants.

Important note: Internal frequency calculation change - Since filtration is now done during case creation, the variant internal frequency is also calculated during case creation. This means that the internal frequency values are frozen at the time of case creation and are no longer updated as new cases are added to the repository. This aligns this annotation with all other variant annotations. The main change here is that novel variants (variants not seen in previous cases) will have a value of N/A, instead of displaying 1 as before. If you use the ‘internal frequency sample count’ filter and want to protect novel variants, please ensure you apply the ‘include N/A’ checkbox to show these variants as well.

This upgrade is only available for samples uploaded after your account has been activated for this change. Previous cases will not be impacted by it.

Coming up next: Filter tree builder - this new feature will enable you to build your quick filters using a graphical tree interface, allowing for improved filtering capabilities and a better user experience.

If you wish to learn more about this upgrade, please contant [email protected].

We're excited to introduce a new feature that streamlines the addition of scientific references to your variant interpretations. With our automated publication association feature, you can now effortlessly add publications directly from the publication tab. Simply click "Add to interpretation," and the publication will be included in your variant interpretation references list

Internal Frequency table upgrade - Franklin now displays for all internal samples if they are of an affected individual or non effected individual.

Editing Variant comments -

You can now edit the comments that you have posted on a variant. Simply click on the pencil icon on the comment, edit the text, and submit the change. Note - you can only edit your own comments.

Protocol assignments improvements::

Assignment Simplification: When marking a protocol step as complete, it will now be automatically assigned to the user who completed it.

Protocol case assignments are now logged in the case history table:

Filtering unassigned cases -

Filtering by assignee now also allows filtering for ‘unassigned’ cases.

Panel filter version display -

In the variant page, on the panel filters, Franklin now displays in barracks the version of the panel used in the case. If this is not the latest version available for the panel, a ‘notice’ icon will be displayed.

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New Somatic Evidence-

RNA variant evidence was updated in our somatic clinical DB.