[ensembl-dev] precedence of snp consequences

Fiona Cunningham fiona at ebi.ac.uk
Mon Jan 24 09:55:48 GMT 2011


 Hello Andrea,

You should really be considering the consequence of the particular
variant  for each transcript that it falls in. This is the correct
thing to do from a biological point of view and this is what the
variant effect predictor does.
For display purposes on the region in detail page only, as we display
of SNPs track that is independent of the transcripts but you should
take the transcript in to consideration when calculating your
consequences. we have internally produced a ranking of consequence so
that the "worst" consequence is used to colour code of variants on
this page but this really is only for display purposes only as an
indication, and has not been independently scientifically verified.
There is no such thing as an "main consequence".

Best regards,

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 23 January 2011 20:01, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Hello
>
> What are the rules that ensembl uses to determine the display_consequence of
> a SNP from all of its possible consequences?
>
> As an example I am looking at a SNP whose main consequence
> (display_consequence) = 3PRIME_UTR and all consequences (consequence_type)
> are given as NMD_TRANSCRIPT, 3PRIME_UTR
>
> Is there a list or ranking you use for consequences to say that 3PRIME_UTR
> is more important than NMD_TRANSCRIPT?
>
> Will the main consequence always be last in the list of the consequence_type
> property?
>
> One reason I ask is because I am trying to apply the same consequence
> ranking to the results returned by the snp_effect_predictor script. That
> script returns one row/line for every consequence in the consequence_type
> field and the order of the consequences in the rows returns seems to be the
> same as the order of the consequences in the consequence_type property. If
> the display_consequence is always last in the list then i can assume the
> last row returned for a transcript variant is the 'main consequence'
>
> thanks
>
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