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The Ensembl Genome Browser

Genetic-Level Variation

Staying on the transcript page, go to the left menu and click on Variant table under the Genetic variation category.


Variation table selection link screen shot

The table will load. This may take a while for some transcripts. To filter your variants, there are several filter options to choose from, including by Consequence Type at the top of the table.

Screen shot of consequence type page.

  • Turn off individual consequence types by clicking on them
  • OR, turn off all consequence types using the All off button then turn on only those you want to see
  • The changes will be made as soon as you click the Apply button
  • To exit the consequence filter, simply click off of it (click on the side of the page, outside the filter table)

Now you will see only your preferred consequences. 

  • You can sort the table by any column. 
  • You will see the amino acid results of the variants, SIFT and Polyphen scores (which may not always concur), evidence, clinical significance (if known), minor allele frequencies (if known), database of source (with links)
  • Export the table in CSV format by clicking the Excel icon in the top right corner of the table

The Variant image (also accessible from the left side menu) is not available for human records, though the link may still show in the menu. This is because there are too many annotated variants for the human genome to make the image useful or easily readable. The Variant Image option is still a feature for non-human genomes, though.


Protein-Level Variation

To view the protein-level variation data, click on Variants in the left hand menu, under Protein information

Similar to the genetic variation table, you will see linked IDs, type, evidence, alleles, consequence and SIFT scores.

A note about alleles and codons in the protein variants table:
The alleles are shown with the base as read on the forward strand, consistent with the genomic coordinates, while the codons are shown as read in the direction of transcription (so in the case of APP, the codons are read from the reverse strand).

What if you want to see all the variants from all the transcripts? 
You can do this at the gene level. Click back on the Gene tab at the top of the page.

Screen shot of protein varian selection link.