The ClinGen Allele Registry provides unique variant identifiers both programmatically (via APIs) and via this search interface. If a variant is not present in the Registry, authorized users may register the variant and get an identifier within seconds. The variants are automatically mapped across known reference sequences and to identifiers from major variant databases.

The current content of the Registry is searchable using HGVS expressions representing nucleic acid or amino acid variants across more than 500,000 reference sequences (genome assemblies, transcripts, amino acid sequences). Alleles can be also queried by locus, gene and ClinVar or dbSNP identifiers. The registry regularly imports variants from ExAC, ClinVar and other databases.

To facilitate wide integration of the registry services with existing software and workflows for variant evaluation, all the functionalities of the registry are exposed via REST APIs. The API also allows for bulk query and registration of variants. Hundreds of variants saved as HGVS expressions can be processed as a batch in less than ten seconds. This will also be extended to VCF file in the near future. For instructions on how to register large batches of variants, follow the "API specification" provided on the home page.

To register new alleles in the Allele Registry, you will need a valid login and password. To create a login, please send an email request to brl-allele-reg@bcm.edu with a preferred login name.

If you have any questions, please do not hesitate to contact brl-allele-reg@bcm.edu.

June, 2019

• Allele registry APIs extended to support GA4GH-refget and GA4GH-VR standards

April, 2019

• HGVS expression with MANE preferred sequence now shows amino-acid mapping
• Added a link to video by ClinGen Education Team on landing page

March, 2019

• Registry landing page updated to include release notes, citation, and, pointers to introductory videos
• Source capitalization fixed for the user contributed link-outs

Feb, 2019

• Allele Registry now shows the MANE preferred transcript at the interface.
• Fixed an issue with protein consequences for inframe insertion/deletion

October, 2018

• Search by dbSNP identifiers now returns more than one hit when applicable. In the previous version, it always used to return one hit.
• Several transcripts were missing associations with genes (e.g. GJB2/GRIA4), as they were missing in the files provided by HGNC. As a result, information for gene was not shown in the variant centric page. Search by that HGNC symbol was not able to retrieve any hit. As a result of this update, they are now correctly associated and search retrieves appropriate results.
• HGVS expression defined as a function of NCBI transcript sequence now provides a link out to recently published Variant Validator (Freeman et al., Human Mutation. 2018;39:61–68). The article and method claim to provide accurate HGVS expressions and correct it on the fly if not appropriate.
• We have developed a semiautomatic pipeline for importing ClinVar update. With this, just a couple of commands will be sufficient to update ClinVar associations in ClinGen allele registry. As a result, we hope to be in sync with ClinVar updates.