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ClinVar inclusion list

ClinVar aggregates information about genomic variation and its relationship to human health. ClinVar variants are annotated directly from Cellbase. The Cellbase and ClinVar versions used in the Newborn Screening Pipeline are listed under Software database versions. ClinVar annotations generated by Cellbase have been validated to ensure that the entries are equivalent to those in the corresponding ClinVar VCF. Details can be found in the validation report (accessible for Genomics England employees only).

To be considered in prioritisation, a variant needs to satisfy all of the following criteria:

  1. The variant (SNV or MNV) is annotated as present in ClinVar OR the variant has the same predicted protein change as the variant in ClinVar (this is not supported for MNVs). Note that we currently cannot distinguish if the variants are an exact or protein match from the annotation outputs.
  2. The variant has at least one pathogenic or likely pathogenic classification in ClinVar.
  3. The variant has no more than one benign or likely benign classification in ClinVar.
  4. Internal allele frequency annotation for the variant is less than 0.05. For MNVs, the allele frequency of at least one of the decomposed variants is below this threshold.

Limitations

See the Limitations of inclusion lists page to understand the limitations involved in prioritised variants from an inclusion list.