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:

Ensembl Variant Effect Predictor (VEP)

GitHub - bch-gnome/hpds_annotation: Annotation pipeline for HPDSGitHub