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.
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.