Already have an HGMD Online subscription? The Human Gene Mutation Database (HGMD) data is now available in Franklin for users with an active HGMD Online subscription.
Access to HGMD features requires a one-time configuration by our Support team - please reach out if you have an active HGMD Online subscription, at [email protected]
Once configured, you’ll have access to the following capabilities (note that some features apply only to new cases):
1. HGMD data on Variant Tile
HGMD classification is displayed as a visual highlight on the variant tile, allowing quick recognition of HGMD-annotated variants.
When you expand the variant tile, the HGMD annotation is shown in more detail, and a “See all HGMD data” link provides direct access to the full HGMD section in the Variant Assessment tab.
2. HGMD Track in Region Viewer
In the Variant Assessment tab of the Variant Interpretation Hub, you can now see a color-coded visualization of SNP variant classifications displayed in the relevant genomic region, alongside existing evidence sources. Hovering over a position will show HGMD evidence together with other available evidence, making it easier to interpret variant significance.
3. New HGMD Widget in the Variant Assessment Tab
A new HGMD widget is available in the Variant Assessment tab within the Variant Interpretation Hub. This widget displays the HGMD classification, reported disease or phenotype, and supporting literature citations, including citation type, support level, and comments. A link in the upper-right corner provides direct access to the HGMD mutation page.
4. New HGMD Widget in the Gene Assessment Tab
A new HGMD widget is available in the Gene Assessment tab within the Variant Interpretation Hub. The widget provides a graphical summary of the gene, displaying a breakdown by mutation type, main disease or phenotype, and classification.
It also includes a detailed mutations table featuring the following information: Nucleotide, Protein, Description, Type, Classification, Reported Phenotypes, Reference, and HGMD Accession. Several fields in the table are interactive and link to related resources: Clicking on the Nucleotide field opens the corresponding Franklin variant popup, the Reference field directs you to the relevant PubMed entry, and the HGMD Accession field links to the corresponding HGMD mutation page.
Filter options at the top of the widget allow you to refine the view by Type or Classification, and a link in the upper-right corner provides direct access to the HGMD gene page.
5. HGMD Classification Filter for SNPs
The HGMD Classification Filter is available on the variant search page and can be applied to SNP variants. This filter can be used in multiple ways - as a dynamic filter, a quick filter, or through the filter tree component - allowing flexible and efficient exploration of HGMD-classified variants.
FAQ
Which HGMD version is available in Franklin?
Generally, Franklin updates its HGMD data in the version following each new HGMD release. Currently, Franklin v88 includes HGMD version 2025.2.
How does Franklin link to the variants in HGMD?
Generally, Franklin links variants to HGMD records by matching their genomic positions according to the relevant reference genome version.