How can I get access to the Pathogenicity Calculator?

Users can easily create a login to access the Pathogenicity calculator.

Create Login

How can I change my password?

Please visit here to change the password. You will need to provide your existing password. If you forgot your password, visit here to reset your password.

Are there tutorials/use cases that may help to introduce to various calculator functionalities?

We created use cases for a new user (here), a recurrent user (here) and a user who wants to register a new allele (a use case showing how to register a new allele is here).

Why am I not able to find the allele that I am looking for?

The Calculator uses ClinGen Allele Registry that regularly updated to include the latest alleles from ClinVar and other sources. It is likely that the allele that you want to use is not available in the registry. Please use the registration functionality to register a new allele. A use case showing how to register a new allele is here.

What if my ACMG/AMP guideline-based conclusion differs from that suggested by the calculator?

Alleles with Uncertain Significance due to conflicting evidence can be asserted as Benign, Likely benign, Pathogenic or Likely pathogenic at user's discretion, upon careful evaluation of evidence. In such cases the difference is acceptable. We would like to hear from you if you encounter other scenarios.

What if I want to use different rules/guidelines for the interpretation of my variants?

Although the Pathogenicity Calculator was developed for making conclusions based on ACMG/AMP guidelines, it can be customized to handle a variety of semi-quantitative guidelines that are similar to ACMG/AMP guidelines. Please let us know if you would like to use custom guidelines (brl-clingen@bcm.edu).

I am already using a variant evaluation system - would it be possible to integrate it programmatically with the calculator so that I can use both systems simultaneously?

All the services working behind the Pathogenicity Calculator are accessible via Application Programming Interfaces (APIs), making it possible to integrate with existing variant curation and evaluation systems. We will soon provide a thorough documentation of these APIs. If you would like to use our services using APIs, you may also let us know (brl-clingen@bcm.edu).