What variant metadata is exposed?

The original sample VCFs are annotated using the Ensembl Variant Effect Predictor (VEP) to determine the effects of each variant, providing additional metadata.

  • Chromosomal location and reference position of variant (hg38)

  • Reference and alternate allele sequence

  • Gene affected by variant

    • Calculated consequence of variant on a given protein sequence (e.g. stop gained, missense, stop lost, frameshift).*

    • The severity of the calculated consequence of a variant on a gene.*

    • Variant class / type (e.g. SNV, deletion, insertion)*

  • Number of patients with this variant in queried subset

  • Number of patients with this variant who are NOT in the queried subset

  • Frequency of variant found in combined gnomAD populations

* These fields are most informative when the user has specified the genomic context, such as the gene of interest.

Some environments also support patient-level data in the variant explorer. In these environments, the right-most columns will contain the zygosity of each patient for each variant.

For more information on VCF file format and our annotation pipeline, visit:

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