Rank model updates for VEP 111

[alkc]

This PR is just material for discussion at today's WGS meeting

Additions to consequence severity ranking:

my %rank = (                                    
    'transcript_ablation' => 1,                 
    'initiator_codon_variant' => 2,             
    'frameshift_variant' => 3,                  
    'stop_gained' => 4,                         
    'start_lost' => 5,                          
    'stop_lost' => 6,                           
    'splice_acceptor_variant' => 7,             
    'splice_donor_variant' => 8,                
    'inframe_deletion' => 9,                    
    'transcript_amplification' => 10,           
    'splice_donor_5th_base_variant' => 11,  <-----------------
    'splice_region_variant' => 12,              
    'splice_donor_region_variant' => 13, <--------------------
    'splice_polypyrimidine_tract_variant' => 14,  <-----------
    'missense_variant' => 15,                   
    'protein_altering_variant' => 16,           
    'inframe_insertion' => 17,                  
    'incomplete_terminal_codon_variant' => 18,  
    'non_coding_transcript_exon_variant' => 19, 
    'synonymous_variant' => 20,                 
    'mature_mirna_variant' => 21,               
    'non_coding_transcript_variant' => 22,      
    'regulatory_region_variant' => 23,          
    'upstream_gene_variant' => 24,              
    'regulatory_region_amplification' => 25,    
    'tfbs_amplification' => 26,                 
    '5_prime_utr_variant' => 27,                
    'intron_variant' => 28,                     
    '3_prime_utr_variant' => 29,                
    'feature_truncation' => 30,                 
    'coding_transcript_variant' => 31,  <---------------------
    'tf_binding_site_variant' => 32,            
    'start_retained_variant' => 33,             
    'stop_retained_variant' => 34,              
    'feature_elongation' => 35,                 
    'regulatory_region_ablation' => 36,         
    'tfbs_ablation' => 37,                      
    'coding_sequence_variant' => 38,            
    'downstream_gene_variant' => 39,            
    'nmd_transcript_variant' => 40,             
    'intergenic_variant' => 41,                 
    'sequence_variant' => 42   <-----------------------------
    );