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Clinical Variant Ark (CVA) inclusion list

Clinical Variant Ark (CVA) is Genomics England’s database that stores small variants (SNVs and Indels) data of the rare disease patients from the 100,000 Genomes Project and NHS GMS whole genome sequencing, the records of interpretation outcomes and variant classifications applied during interpretation, as well as the patient’s clinical data, such as clinical indication and HPO terms. CVA variants are sourced from the live database using the CVA API within the pipeline.

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

  1. The variant is present in CVA, OR the variant has the same predicted protein change as the variant in CVA. Note that we currently cannot distinguish if the variants are an exact or protein match from the annotation outputs. CVA does not support MNVs and they are reported separately so these would be prioritised as individual SNVs.
  2. The variant has at least one pathogenic or likely pathogenic classification in CVA outcome questionnaires.
  3. Internal allele frequency annotation for the variant is below 0.05.

Limitations

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