SOP Section 5.3
Before beginning an interpretation, confirm you are logged in to the desired Affiliation. For assistance, see Affiliations.
If an interpretation is started in the wrong Affiliation, please email clingen-helpdesk@stanford.edu.
To begin an Interpretation in which you can evaluate the evidence according to the ACMG criteria, select from the evidence view.
You will then be asked to agree to the VCI Submission Policy Agreement:
Click Agree to enter interpretation mode.
If you select Disagree, you will return to evidence view.
An interpretation is specific to the curator who creates it and can only be viewed or edited by that curator or the affiliation the curator is curating under. Starting an interpretation will create a record on the dashboard.
SOP Section 6.1
When you are ready to evaluate disease-specific criteria for your interpretation, click or to open the "Add Disease" selection screen.
Enter the desired ID and click "Retrieve from OLS". Verify your disease term and click save.
For assistance using MONDO Search, see MONDO Search Help
It's highly recommended to use an ontology term, but if there is no MONDO term, then a free text term may be entered for the disease. If you are unsure about an appropriate disease term, please contact us at clingen-helpdesk@lists.stanford.edu and we will be happy to assist.
Click on "Add free text term" to enter a free text term (up to 100 characters in length). You must also provide a set of HPO terms (preferred) and/or a definition for the term you are entering.
For assistance using HPO Search, see HPO Search Help
NOTE: If another curator enters a different phrase for the same ID, the interface will not be able to determine if they are equivalent, this is why we strongly suggest using the MONDO ontology terms.
After saving, you will see the associated disease listed under the variant, as well as under "My Interpretation" and the Disease+ button will be replaced with
SOP Section 6
Each variant curation record may be associated with one disease, one mode of inheritance, and one specification document. Each of these may be selected and modified while the record in is in progress by using the grey boxes in the interpretation progress bar.
SOP Section 5.3
Once in Interpretation mode, the following options will appear:
A. Click to view a summary of all criteria evaluations.
B. Click to view the complete history of curation actions for this interpretation record. Note: It will not include actions from other interpretations of this variant.
F. The Progress bar indicates the strength of criteria met and the auto-calculated pathogenicity.
G. The Criteria bar displays all ACMG criteria codes. Scroll over a code to display its description. Click on a code to navigate to the pertinent section in the VCI.
The Evidence Tabs will now be populated with the ACMG criteria evaluations where you can indicate whether an individual criterion is “Met” (see Evaluating Criteria).
SOP Section 6.3
To add the mode of inheritance click which opens the Inheritance selection screen.
Select mode of inheritance, and then, if applicable, select an adjective.
After saving, you will see the mode of inheritance under the variant, and the Inheritance button will be teal.
SOP Section 6.4
To add a specification document click on the button.
The drop down menu will display all specification documents that are applicable to the ClinGen approved VCEP you are curating as a part of.
If you are not curating under an affiliation, all current specification documents are displayed.
For more information or questions about Specification Documents, see the CSpec Registry or email brl-cspec@bcm.edu
C. Click to add a specification document to the curation
D. Click or "Add Disease +" under "My Interpretation" to associate a disease with the variant.
E. Click to add mode of inheritance.
