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Should ENSEMBL up- and downstream variants be classified as genic or non genic?

According to the Variant Effect Predictor tool from Ensemble, the consequence types upstream gene and downstream gene variants are located within 5 Kb from the transcript. I would like to create 2 categories, "genic" and "non genic" and include up- and downstream gene variants (as well as all other consequence types from ENSEMBL) into one of them. Where to include up- and downstream variants?. Thanks very much

ensembl
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updated by Ben Moore Ben Moore • written by Mr Locuace Mr Locuace

1 answer

Hi there,

Ensembl uses Sequence Ontology (SO) terms tho describe the consequences of variants. The upstream/ downstream consequence type is defined as being within 5kb of the transfer: http://www.sequenceontology.org/browser/current_svn/term/SO:0001631

So, a particular variant could be an upstream variant of all of (or a subset of) the different transcripts of a gene.

For example, if you consider the different transcripts of BRCA2 (http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32315474-32400266) a single variant might be an upstream variant of the BRCA-001 transcript, but not of the BRCA2-003 transcript.

Technically the upstream/downstream variants fall outside of the defined gene boundaries, but the decision whether to include them in one category or another for a particular analysis really depends on the analysis you wish to perform and the definitions of variants you wish to apply during your analysis.

Best wishes

Ben Ensembl Helpdesk

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written by Ben Moore Ben Moore

Thank you very much, Ben !

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written by Mr Locuace Mr Locuace

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