Tools and utilities that enable the use of the variant pathogenicity interpretation model

The interpretation model is ClinGen's way to send and receive information about variant pathogenicity. Here are some tools that can help those implementing the model, and some tools that use the model.

Interpretation Creator

Github Repository

Interpretations in this model are encoded in JSON-LD. This python package helps to correctly create such JSON-LD messages. Users of the library can build interpretation objects in code, and then serialize correct JSON-LD.

VCI Transformation

Github Repository

The ClinGen Variant Curation Interface produces JSON-LD documents, but not in the ClinGen interpretation format. This script, based on the interpretation_json library, converts interpretations from the native VCI format to the ClinGen format.

Clinvar Submission

Github Repository

ClinVar accepts interpretation submissions using its own spreadsheet-based format. This tool consumes JSON-LD files in the ClinGen interpretation format, and converts them into valid ClinVar spreadsheets, which can then be manually submitted to ClinVar.