Submission of Variants to the ClinVar portal
Requirements
Make sure to
register a user to the
ClinVar submission portal.
If your Organization is not already present in ClinVar you should follow the instructions to
register a submitting Organization to the same portal.
The first time an organization is registered in the ClinVar Submission Portal, the content will be reviewed, so it will take some time before getting approved in order to start a variant submission.
Automatic submission
Once the requirements above are fulfilled you could submit manually using files uploaded to the ClinVar submission portal. See the heading below. You can avoid this extra file handling step by submitting directly via API instead. Submission by API requires a service account key for the submitting organization and an API key associated with it.
Follow the instructions provided on the API pages to obtain a valid key for the service account.
Once you are satisfied with the content of your submission in Scout, you can submit your variants using the ClinVar API. If you obtained a submission ID from ClinVar (format: "SUB999999") and you want to use it for the submission, you can save it using the "Update ID manually" button:

Alternatively you can leave the Submission ID blank, so it will be retrieved directly from the ClinVar API once a successful submission has been processed..
To send the submission object to ClinVar using the API click on the Submit to ClinVar button:

If the submission object is processed without errors then it will be marked as "submitted" in Scout, otherwise eventual validation errors should be displayed on top of the page.
Manual submission
Once you have registered to the ClinVar portal as a submitter for a given Organization, you can start a new manual submission by using the "Upload new file submission" button from the submission page.
This button is a link to a multi-panel (4 panels) submission page. The first panel (submission information) has a precompiled field named "Submission name".
Fill in submission forms in panel 1 and 2, respectively named "Submission information" and "Organization". In the "Submission format" in panel 1 make sure to select the value "Comma-separated values".
Assembly name fields should be filled in before proceeding further with the submission.
You'll need to register the Submission Name obtained from the ClinVar portal in order to download variants and casedata submission files.

Download the files above (either the variants .csv file or the variants .csv + the casedata .csv files) from Scout and upload them in the "Submission Files" field in the third panel of the submission.
Note that if you edit these files in Excel you need to save them in the correct format: comma-separated columns. Default settings should probably work fine if your software's locale is US English.
If this is not the case you might need to change your software's region settings to use US English before exporting these tables.