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Variation Table (Gene)

Short sequence variations are shown by consequence type in the Variation Table.

This view shows all the variant consequences in a gene. If the same variant falls in several transcripts within the same gene, a new row will be displayed for each transcript. Therefore, this number reflects the number of variant consequence types across the transcripts. 

The SO term accession numbers (e.g. SO:0001792) are also available and linked to the Sequence Ontology Browser (MISO).

If you show a table for a variation consequence type, the columns will be as follows:

  • ID - The identifier of this particular genetic variation in an external database. Frequently, this will be an rs identifier, a reference SNP from NCBI dbSNP.
  • Chr:bp - Chromosome name and base pair co-ordinates
  • Alleles - Possible nucleotides at the position listed in the Chr:bp column. These are reported for the forward strand of the genome sequence
  • Global MAF - The global minor allele frequency is calculated using all 1000 Genomes Phase 3 data for this SNP, across populations
  • Class - For example, Single Nucleotide Polymorphism (SNP) and Insertion-Deletion (InDel)
  • Source - Original database/project from which the variation was imported
  • Submitters – The original submitters of the data
  • Evidence Data that support a variant and suggest how reliable the variant is. A summary of evidence status is available on our documentation on Variation data.
  • Clinsig – A term assigned by dbSNP and ClinVar that indicates pathogenicity or drug response. A list of clinical significance terms can be found on our documentation on Variation data.
  • Type - Consequence type based on SO (Sequence Ontology) terms. Click on Configure this page at the left to change the consequence types
  • AA - (Amino acid) Possible amino acid(s) (if any) resulting from the allele(s) at the position of the variation. More than one amino acid will be listed for a non-synonymous variation
  • AA coord - (Amino acid coordinates) The position of the amino acid (AA) within the protein sequence. The number refers to the position of the variation in the codon (1, 2, or 3).
  • SIFT - Prediction of variation effect on protein function by SIFT
  • PolyPhen - Prediction of variation effect on protein function by PolyPhen
  • Transcript - The specific Ensembl transcript for the gene of interest in which the variation shows the consequence type

You can order the table by the columns by clicking on the up/down arrows by the column titles. Filters in the top grey bar allow you to filter the data by SNP type.

Go to the Variation Image for a graphical view.