[ensembl-dev] Variant/Phenotype assocation plugin: How to output annotation per consequence correctly?

[Guillermo Marco Puche]

Dear devs,

I've been using this plugin I made with the help of Will McLaren: 
https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0
I'm pretty happy with the results however I would like to improve it. At 
this moment plugin outputs the selected phenotypes for all the 
consequences per transcript. However this is not right.

If I annotate the following record:

  * chr11    128911444    .    T    C

I get ClinVar information for all the transcripts consequences of the 
variant. However If I'm not wrong I should only output ClinVar for those 
consequences with same RefSeq as described by ClinVar, in this case 
"NM_000890.3" associated to RCV000126421.3.

I don't understand exactly how does Ensembl handles Phenotype 
information and if this kind of check is possible. The point should be 
only output phentoypes not only based on variation but check that 
transcript between phentoype and variation is the same.

Regards,
Guillermo.

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