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What is ClinVar class?

Clinvar class is the clinical significance value given by ClinVar database:

Guidance for use in ClinVar SCV records

  • Benign - As recommended by ACMG for variants interpreted for Mendelian disorders.
  • Likely benign - As recommended by ACMG for variants interpreted for Mendelian disorders.
  • Uncertain significance - As recommended by ACMG for variants interpreted for Mendelian disorders.
  • Likely pathogenic - As recommended by ACMG for variants interpreted for Mendelian disorders.
  • Pathogenic - As recommended by ACMG for variants interpreted for Mendelian disorders.
  • drug response - A general term for a variant that affects a drug response, not a disease. We anticipate adding more specific drug response terms based on a recommendation by CPIC.
  • association - For variants identified in a GWAS study and further interpreted for their clinical significance.
  • risk factor - For variants that are interpreted not to cause a disorder but to increase the risk.
  • protective - For variants that decrease the risk of a disorder, including infections.
  • affects - For variants that cause a non-disease phenotype, such as lactose intolerance.
  • conflicting data from submitters - Only for submissions from a consortium, where groups within the consortium have conflicting interpretations of a variant but provide a single submission to ClinVar.
  • other - If ClinVar does not have the appropriate term for your submission, we ask that you submit "other" as clinical significance and contact us to discuss if there are other terms we should add.
  • not provided - For submissions without an interpretation of clinical significance. The primary goal of ClinVar is to archive reports of clinical significance of variants. Therefore submissions with a clinical significance of "not provided" should be limited to:
    • "literature only" submissions that report a publication about the variant, without interpreting the clinical significance
    • "research" submissions that provide functional significance (e.g. undetectable protein level) but no interpretation of clinical significance
    • "clinical testing" submissions from clinics or physicians that provide additional information about individuals with the variant, such as observed phenotypes, but do not interpret the clinical significance