[ensembl-dev] About the rank of "Coding unknown" in the VEP consequence output

[Huang Yen-Hua]

Hi Ensembl dev.,

I am using VEP to list the possible consequences of SNPs and just notice
that the rank of "coding unknown" (16) is higher than that of  
"Synonymous
coding" (15), as indicated in  
Bio::EnsEMBL::Variation::Utils::Constants as
well as on http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences 
.

This looks a bit strange to me. I cannot clearly get the reason about  
why a
synonymous change may cause a more severe consequence than a coding
unknown case that is now also referred to as "coding_sequence_variant"
in the SO-term system.

Best,
Yen-Hua

======================
Yen-Hua Huang, PhD
Institute of Biomedical Informatics
National Yang-Ming University
Taipei, Taiwan
======================