[ensembl-dev] precedence of snp consequences

[Andrea Edwards]

Please feel free to ignore this question, unless of course you feel 
others may benefit from an answer. From my point of view:

-The consequence precedence rules seem common sense based on the large 
sample i have looked at (though these's always the chance there's some 
obscure combination i've overlooked)
-if there are rules for how the consequences are ordered in the 
consequence_type field I can't use them so its a moot point for me 
personally. The main consequence isn't something as simple as the first 
or last one in the list and the consequences aren't ordered alphabetically.

cheers


On 23/01/2011 20:01, Andrea Edwards 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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