The goal of VariantExplorer is to facilitate identification of clinical significance interpretation discrepancies in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/), a submitter-driven repository that archives reports of the relationships among genomic variants and phenotypes submitted by clinical laboratories, researchers, clinicians, expert panels, practice guidelines, and other groups or organizations. Given the large number of submitters to ClinVar, many variants have interpretations from multiple submitters and those interpretations may not always agree.
By displaying how the full set of variant interpretations from a specific submitter compares to all other submitters (or to another specific submitter), VariantExplorer helps users view the types and levels of discrepancies in ClinVar. The submitter-specific Clinical Significance Breakdown Tables (seen below) displays pair-wise counts of discrepant interpretations, including confidence discrepancies (such as Benign vs Likely benign or Pathogenic vs Likely pathogenic). For example, the table below indicates there are 12 variants in ClinVar interpreted as Likely benign by Submitter A and interpreted as Uncertain significance by Submitter B. By displaying the discrepancies in this manner, VariantExplorer hopes to facilitate resolution of interpretation discrepancies.
The discrepancy data in VariantExplorer can be viewed from four different approaches: