Version 97 Updates

Release Date: October 12, 2026

We are happy to introduce several enhancements and new features in our latest update:

In germline cases, Variant Evidence is now accessible directly from the variant popup side panel for SNP variants. The side panel allows you to view, add, and delete evidence for a variant - including types and detailed notes - mirroring the functionality already available on the variant tile.

This enhancement lets you manage evidence in one place while viewing the detailed information in the variant popup. As before, variant evidence propagate across cases (both existing and future), and any propagated evidence will display a specific indicator.

Deletion-insertion (delins) variants are now better supported when manually added in germline or somatic cases, as well as in variant search. This includes supporting delins whose boundaries fall within introns, that span one or more introns, or that extend into the 5′ or 3′ UTR, as well as larger delins spanning tens of kilobases. The input format is based on c-dot (c.); when an input format cannot be resolved, an informative error message will now be displayed.

In workflows that selectively target the CYP21A2 gene, such as gene-specific amplicon approaches that distinguish it from the CYP21A1P pseudogene, a Franklin assay can now be configured to align reads against a reference in which CYP21A1P is masked. This ensures that CYP21A2 reads map to the gene and not the pseudogene, so CYP21A2 variants in the case are called accurately. This improvement is available for hg38 assays. To configure a relevant assay, please contact our support team ([email protected]).

CMA single cases created from Illumina IDAT files now support sex detection based on Illumina GenCall. Calling and annotation will be performed based on the sex you input; if you leave the sex unspecified (unknown), Franklin will use the detected sex. The Sex Detection quality control (QC) metric is now supported, showing the detected sex and alerting you to discrepancies between provided and detected sex or if the sex is undetermined. Additionally, the Report can now include the detected sex under the QC section. Note: in the scenario where both user input and the detected sex are unknown, annotation defaults to male; this is applied as the conservative default so that X-linked and Y-chromosome findings could be surfaced and evaluated. To access an IDAT assay, please contact our support team ([email protected]).

Resolved an issue where in some scenarios, the “Filter Tree Labels” column header was missing in the CSV export from Variants tab for SNP in germline cases.