HumanEnsembl Home

Explore this variation

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 variation for short variants.
  • Alleles - The allele found on the forward strand of the reference assembly is shown first. Any alternate alleles are then displayed. For example, G/C indicates that the reference allele on the forward strand is G, and a C allele has also been detected at this position. Note: Ambiguity or IUPAC codes indicate the possible alleles. See the table at the bottom of this page. Minor Allele Frequency (MAF) refers to the lowest allele frequency of a sequence variant (such as a SNP). The global MAF is calculated using the allele frequences across all 1000 Genomes Phase I populations.
  • Location - The location (chromosome, or scaffold, and basepair) of the variation is indicated, and a link is provided to the Region in Detail view. 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 dbSNP and ClinVar that indicates pathogenicity or drug response.
  • Synonyms - Other databases and projects cataloguing the same variation are listed. Any names of the variation within the alternate source are shown.
  • 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 - Any platforms such as Illumina or Affimetrix chips with this variant.

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

IUPAC Ambiguity Codes