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Explore this variant

Example page

This page offers a top panel of information specific to the variant. Graphical icons are presented that lead you to more specific variant data, also accessible from the links at the left. The links in the left hand menu have a corresponding icon. It's your choice how to navigate through the variation displays.

Top Panel

From the top of the view, the following information can be found:

  • Variant ID and Original Source - The variant can be a SNP, insertion, deletion, structural variant, or a somatic mutation. An ID from dbSNP (rs...) is used preferentially to name the variant for short variants.
  • Alleles - The allele found on the forward strand at this location is shown first. Any alternate alleles are then displayed. For example, G/T indicates that the reference allele on the forward strand is a G, and a T allele has also been detected at this position. Ancestral alleles, available for primates, are calculated based on multi-species alignments. Minor Allele Frequency (MAF) refers to the second highest allele frequency of a sequence variant. The global MAF is calculated using all 1000 Genomes Phase 3 samples. The highest population MAF is the highest frequency observed in any available population for the minor allele. All populations are checked, for human this includes sub-populations in the 1000 Genomes Phase 3 and gnomAD projects. This provides a clearer guide as to how common the allele is in any reference panel.
  • Change tolerance – Conservation scores are calculated using GERP on the Ensembl Multiple Sequence Alignments of whole-genomes. Positive scores represent highly-conserved positions while negative scores represent highly-variable positions. The CADD score, as available from the CADD project website, is also displayed for human. Higher CADD scores are more likely to be deleterious.
  • Location - The location (chromosome, or scaffold, and basepair) of the variation is indicated, and a link is provided to the Region in Detail view. The Variant Call Format (VCF) location is also shown (Chromosome, basepair coordinate, variant ID, reference allele and alternate allele). If more than one location is available, the variant maps to multiple locations.
  • Co-located - Other projects and database that have the same variant, and the name of the variant within the project.
  • Most severe consequence - One variant may have multiple consequences on various transcripts. One consequence is ranked highest according to its effect and/or location with respect to a transcript. For example, a missense mutation will be shown in this field even if in some transcripts, the variant has a consequence type of 'intronic'. 
  • Evidence Status - Ensembl assigns a status to variants that reflect the reliability of the data; for example if it has come from the 1000 Genomes project, or if it is polymorphic in multiple samples. 
  • Clinical significance - A term assigned by ClinVar that indicates pathogenicity or drug response.
  • Synonyms - Other databases and projects cataloguing the same variation are listed. Any names of the variant within the alternate source are shown.
  • Variant with equivalent alleles - Deletions and insertions can sometimes be functionally identical to each other, for example if there is a repeated base in the genome, variants may be reported that are deletions of different bases in the repeat. They are kept separately in the database because different external data may be linked to them, however they result in the same sequence so can be considered functionally identical. If a variant is listed here, you should check the other variant for annotation such as phenotypes or population genetics, as this information will be relevant to both variants.
  • HGVS name - If nomenclature for this variant from HGVS is available, it will be shown here. A guide to HGVS symbols can be found at the HGVS website.
  • Genotyping chips - The names of any genotyping arrays from Affymetrix or Illumina which contain assays for this variant.

Please see the Ensembl variation documentation for more information such as source of variants, and consequence types (effect on genes and transcripts).