Variant Browser

Overview

The Variant browser allows you to view and filter variants for your chosen study using multiple parameters, which can be found in the left-hand menu. The filters available are:

Filters

Applying filters

• Studies

  • For studies on the within the same project (RD38 & CG8) you can apply AND/OR logic to filter for variants present in both studies or either one of the studies. Select the logic and tick the appropriate box fir your study of choice

• Genomic

  • Chromosomal location (by genomic coordinate)

  • Feature IDs (genes, SNPs, transcripts)

  • Gene disease panels (genes included in the chosen PanelApp panels)

  • Biotype (gene or transcript type)

  • Variant type - SNV (single nucleotide variant), MNV (multiple nucleotide variant), CNV (copy number variant), SV (structural variant) or INDEL (insertion/deletion)

• Population frequency

  • Population frequency as calculated overall or by population group in the 1000 Genomes and gnomAD databases

• Consequence type

  • Consequence type SO (Sequence ontology) terms. You can filter for all Loss-of-Function terms here

• Deleteriousness

  • Deleteriousness of variant using prediction tools SIFT, Polyphen and CADD (NB that CADD is only available in GRCh37 studies)

• Conservation

  • Conservation score as calculated by PhyloP, PhastCons and Gerp.

• Gene ontology

  • Gene ontology terms describing gene function

• Phenotype-disease

  • HPO (human phenotype ontology) accession IDs

  • ClinVar accession IDs

  • Full-text search on HPO, ClinVar, protein domains or keywords, and some OMIM and Orphanet IDs

Once you have defined your filters, click Search to show the resulting variants in table format, as in the screenshot below. (Summary format is not yet available.)