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Variation Table (Transcript)

Short sequence variations are displayed for a transcript (splice variant) in the Variation table.

This view provides a summary of all short sequence variants for a specific transcript (splice variant). The variants are summarised by "consequence type" (the location within the transcript or effect on the coding/splicing sequence). We use SO terms from the Sequence Ontology project, described here, and the ontology of the consequence type may be changed using the Configure this page tool button at the left of the view.

Click on "Show" next to the variation consequence for a table of a specific variation type.  Export the table using the CSV icon at the top right of the table.

The variation sources shown in the table and diagram can be changed using the configure this page tool button at the left. By default, not all intronic variations are shown. To see a full display of intronic variations, select "Intron Context" and change it from 100bp to "Full Introns" in the menu.

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 - Global minor allele frequency, calculated using all the 1000 Genomes Phase 3 data for this variant.
  • Class - Single Nucleotide Polymorphism (SNP) and Insertion-Deletion (InDel), for example.
  • Source - Original database/project from which the variation was imported.
  • 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.
  • Clinical significance 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
  • 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 co-ordinate - 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
  • CADD  - Prediction of variant effect on protein function by CADD
  • REVEL  - Prediction of variant effect on protein function by REVEL
  • MetaLR  - Prediction of variant effect on protein function by MetaLR
  • MutationAssessor  - Prediction of variant effect on protein function by MutationAssessor