We are happy to introduce several enhancements and new features in our latest update:
Franklin Community Forum is Available
The Franklin Community Forum is now open to all users. The forum is a dedicated space to connect with genomics professionals worldwide, discuss challenging variants, and share workflow guidelines. It also gives you a direct line to the Franklin product and clinical teams - allowing you to share feedback, ask questions, and help shape the future development of the Franklin platform.
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Improved HPO Synonym Mapping
Additional HPO scopes are now used by the model - broad and narrow synonyms - expanding recognized clinical terms and colloquial expressions. External sourced outdated HPO synonyms have been removed.
Note: As part of this update, terms outside the official HPO vocabulary are no longer supported. Uploading a sample sheet with unsupported phenotypes will result in an explanatory error message. The autocomplete of the Phenotypes field will suggest only official term.
Refinement of BA1/BS2 classification rule
The BA1 and BS2 classification rules have been refined to better match the ClinGen recommendation for exclusion of specific variants (see PMID: 30311383). When reviewing a relevant variant, you will see a clear note in the BA1/BS2 rule, indicating the variant presence in ClinGen’s exclusion list. This enhancement better aligns Franklin's BA1 and BS2 classification rules with ClinGen recommendations.
Refined SMA Silent Carrier Status Logic
The SMA (SMN) biomarker logic now only indicates the "Silent carrier (2+0)" state when both conditions are met: there are exactly two SMN1 copies, and the c.*3+80T>G predictor variant is present. If more than two SMN1 copies are detected, the silent carrier status is not shown, and only SMN1 and SMN2 copy number texts are displayed. This update applies to new and reanalyzed germline cases, increasing the clinical relevance of the biomarker logic.
Improved Phenotype Category for Disease Application for Genotype-Phenotype Scoring
The main phenotype category mechanism utilized by Franklin’s genotype-phenotype model has been updated and extended. This provides more accurate lowering of scores for weak genotype-phenotype connections, improving the overall precision of variant ranking. For more information on main phenotype categories in the genotype-phenotype model, please visit the following Help Center article.
HGMD Database Update to v2026.1
HGMD data, available for users with an active HGMD Online license configured in Franklin, has been updated to reflect HGMD v2026.1, the latest available version.
Classification Tags Included in Workbench Export and API
When exporting Workbench results using “Export WB results” from the case menu, a "Classification Tags" column will now be included in all variant sheets of the output file. The same tags are now also included in the corresponding sections of the “Get WB results” API response. This enhancement helps you track, filter, and manage variant classifications more effectively in downstream analyses and reporting.
Bug Fixes:
Viewing Uploaded Variants in Knowledge Base
Resolved an issue where in some cases, SV uploaded to the Knowledge Base were not displayed in the Knowledge Base after the upload. Uploaded variants are now displayed in a more timely manner after the upload is complete.
Removing Compounds from Reports and Workbench Bins
Resolved an issue where compound variants (SNP-SNP and SNP-SV) could not be removed from the Report or from Workbench bins. You can now successfully remove these variants from both places.