Frequently Asked Questions

Variant Curation Expert Panels (VCEPs) evaluate evidence to classify a genomic variant on a spectrum from pathogenic to benign with respect to a particular disease and inheritance pattern. The VCI is a tool used for this process, and also supports the ClinGen FDA-recognized curation workflow. For more information, please see About Variant Curation.

Gene Curation Expert Panels (GCEPs) implement an approved process of evaluating the strength of evidence supporting or refuting a claim that variation in a particular gene causes a particular disease. The GCI is a tool used for this process. For more information, please see About Gene-Disease Clinical Validity Curation.

It is expected that all users of the VCI are using it to curate variants and in doing so, add to the pool of evidence for use by all. As such, access to the VCI is mostly limited at this time to both Variant Curation Expert Panel (VCEP) and curation affiliation members, however we encourage all users who will use the interface to curate variants as part of their work. At this time, access to the GCI is limited to members of ClinGen Gene Curation Expert Panels (GCEPs).

Our demo/test site is accessible at curation-test.clincialgenome.org, and the demo VCI and GCI is available to the wider public. Please see below for more information on the demo sites.

ClinGen welcomes volunteer curators! Training is held quarterly for community curators interested in baseline annotation. For more information on volunteering to curate, please see the ClinGen Community Curation Working Group (C3 WG) page or contact volunteer@clinicalgenome.org with questions. The volunteer process involves filling out a brief survey to indicate your interests, expertise, and desired level of involvement, and the C3 team uses this to pair volunteers with an appropriate curation activity and/or an Expert Panel.

If you are interested in curating for a particular expert panel, you can also contact that panel's coordinator from the expert panel's page on the ClinGen website.

In order to register for the interface, select “Login” on our production site (curation.clinicalgenome.org) and then select the “Create Account” button, following the registration process from there. Please note that the email address and password that you enter will be case sensitive. You can also register for our test site (curation-test.clinicalgenome.org) following the same process - please note that separate accounts are needed for the test and production sites. We encourage users to register with email addresses that they do not anticipate will expire (e.g. using an alternative to a student email address that will be retired upon graduation). We approve registration requests every few days. In order to expedite your access, please send us a message at clingen-helpdesk@lists.stanford.edu once you’ve finished the registration and email confirmation process. Please let us know in your message if you are part of any ClinGen expert panel or ClinGen curation affiliation so that we can confirm and add this to your account.

Please note that at this time, a curation affiliation is needed to access the GCI.

The test site is designed for users to explore and practice using the interface rather than to curate. Data in the test site is periodically deleted. Please note that separate accounts are needed for the test and production sites, and the Stanford ClinGen team is unable to transfer data between the two. Users should not curate in the test site.

It is expected that all users of the VCI and GCI are using it to curate variants and genes respectively and in doing so, add to the pool of evidence for use by all. As such, we request that users who would like access to the VCI for reasons other than curation for ClinGen to please contact the helpdesk at clingen-helpdesk@lists.stanford.edu with their name, email, background knowledge of variant curation, and what they would like to use the interface for, and we would be happy to assist. Users may also explore our test/demo site at curation-test.clinicalgenome.org if they wish to gain familiarity with the interface itself. Anyone interested in curating genes in the GCI should contact genecuration@clinicalgenome.org for more information on ClinGen's gene curation work.

We request that if you are using the VCI for your variant classification work you cite our flagship VCI publication, "ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines." For general information about citing ClinGen in your work, see the ClinGen Terms of Use.

Yes! You can find us at https://github.com/ClinGen

Updates to the VCI and GCI are posted to the gene-and-variant-curation-tools repository wiki at https://github.com/ClinGen/gene-and-variant-curation-tools/wiki/GCI-&-VCI-Updates.

Please send our team a message at clingen-helpdesk@lists.stanford.edu and let us know in your message if you are part of any ClinGen expert panel or ClinGen curation affiliation so that we can confirm and add this to your account.

Please copy your expert panel’s curator on the email if you need a VCEP or GCEP curation affiliation added, as this allows us to more quickly confirm your affiliation.

At this time, it is difficult to change the email on an account, so we encourage users to register with an email address they do not expect to be retired. If you lose access to an email address, please register for an account under your new email address, then contact our helpdesk at clingen-helpdesk@lists.stanford.edu with your name, your old email, and your new email, and we will transfer the account.

Due to the frequency of requests to transfer curations from one account to another, at this time we cannot support multiple accounts for one user.

In many cases, the account was registered with some form of capitalization. Please note that your email and password are both case sensitive - that is, if you registered under NAME@EMAIL.COM or Name@Email.com, you will not be able to log in as name@email.com. If you are unable to log in after checking capitalization and confirming your email address, please contact the helpdesk at clingen-helpdesk@lists.stanford.edu.

Please contact the helpdesk at clingen-helpdesk@lists.stanford.edu with your name, registered email address, and a description and screenshot of your error.

Either contact your expert panel’s coordinator, who will then contact the helpdesk, or send us an email at clingen-helpdesk@lists.stanford.edu and copy your coordinator on the email. Please be sure to include your name, email address, and the full name (not acronym) of the expert panel you need the affiliation for.

Please ensure that your members have registered for an account for our production site at curation.clinicalgenome.org - accounts must be created separately for the test and production sites. Once you have confirmed they have registered, please send a message to the helpdesk at clingen-helpdesk@lists.stanford.edu including the full name (not acronym) of the affiliation, including whether your expert panel is a VCEP or GCEP, and for each member to be added, their name and email address used for registration.

Please send a message to the helpdesk at clingen-helpdesk@lists.stanford.edu including the full name (not acronym) of the affiliation, including whether your expert panel is a VCEP or GCEP, and for each member to be removed, their name and email address used for registration.

If you were already logged in before the curation affiliation was added, the affiliations may not have updated. Please log out of all open instances of the VCI/GCI interface on your computer. When you log back in you should be able to select “Change Affiliation” in the top right of the screen and see the new affiliation listed. If that fails, check if you may have left open a version of the interfaces on another tab on your computer or email us at clingen-helpdesk@lists.stanford.edu.

At this time, we can create curation affiliations for particular groups at institutions, but do not have generic institution-based affiliations. If you are interested in setting up an affiliation for your lab group, please contact the helpdesk at clingen-helpdesk@lists.stanford.edu.

We can transfer curations within the interface, please send an email to clingen-helpdesk@lists.stanford.edu with the following information:

• Your name and email address you use for the VCI/GCI.

• Whether this was done in the VCI or GCI

• For VCI entries: the variant ID/name.

• For GCI entries: the Gene HGNC symbol, associated disease and mode of inheritance.

• URLs of the each curation done under the incorrect affiliation.

• Full name of the affiliation each record was curated under.

• Full name of the affiliation the records should have been curated under.

Please note that in some cases we may need to delete the record and you may need to recurate under the correct affiliation.

Because the test and production sites are separate, we cannot transfer any test curations into production. In cases like these, you will need to recurate in the production site.

Please try logging out of the interfaces and back in. You may also want to try a hard refresh on your browser (you can google how to do this based on your specific internet browser). If this does not work, please email us at clingen-helpdesk@lists.stanford.edu with the following information:

• What type of operating system (Mac, Windows, etc.) your computer is running, including the name and version.

• What browser and version you were using when you noticed the issue.

• When you saw the issue.

• A detailed description of the behavior you are reporting. Please add screenshots if possible and report any error messages verbatim.

• Whether logging in/out of the interfaces or hard refreshing your browser fixes the behavior.

• Whether you’ve noticed this behavior on certain networks (i.e. things seem fine on your home wifi but when at work you’re seeing the behavior).