genmod_SV.txt

[Version]
  version = 1
  name = rank_model_publication

[Categories]
 [[Consequence]]
   category_aggregation = sum

[MostSevereConsequence]
  field = INFO
  data_type = string
  category = Consequence
  record_rule = max
  separators = '&',
  info_key = CSQ
  csq_key = Consequence
  description = The most severe consequence for this variant

  [[transcript_ablation]]
    score = 5
    priority = 1
    string = 'transcript_ablation'

  [[initiator_codon_variant]]
    score = 5
    priority = 1
    string = 'initiator_codon_variant'

  [[frameshift_variant]]
    score = 5
    priority = 1
    string = 'frameshift_variant'

  [[stop_gained]]
    score = 5
    priority = 1
    string = 'stop_gained'

  [[start_lost]]
    score = 5
    priority = 1
    string = 'start_lost'

  [[stop_lost]]
    score = 5
    priority = 1
    string = 'stop_lost'

  [[splice_acceptor_variant]]
    score = 5
    priority = 1
    string = 'splice_acceptor_variant'

  [[splice_donor_variant]]
    score = 5
    priority = 1
    string = 'splice_donor_variant'

  [[inframe_deletion]]
    score = 5
    priority = 1
    string = 'inframe_deletion'

  [[transcript_amplification]]
    score = 5
    priority = 1
    string = 'transcript_amplification'

  [[splice_region_variant]]
    score = 5
    priority = 1
    string = 'splice_region_variant'

  [[missense_variant]]
    score = 5
    priority = 1
    string = 'missense_variant'

  [[protein_altering_variant]]
    score = 5
    priority = 1
    string = 'protein_altering_variant'

  [[inframe_insertion]]
    score = 5
    priority = 1
    string = 'inframe_insertion'

  [[incomplete_terminal_codon_variant]]
    score = 5
    priority = 1
    string = 'incomplete_terminal_codon_variant'

  [[synonymous_variant]]
    score = 5
    priority = 1
    string = 'synonymous_variant'

  [[non_coding_transcript_exon_variant]]
    score = 5
    priority = 1
    string = 'non_coding_transcript_exon_variant'

  [[mature_mirna_variant]]
    score = 5
    priority = 1
    string = 'mature_mirna_variant'

  [[non_coding_transcript_variant]]
    score = 5
    priority = 1
    string = 'non_coding_transcript_variant'

  [[regulatory_region_variant]]
    score = 5
    priority = 1
    string = 'regulatory_region_variant'

  [[upstream_gene_variant]]
    score = 0
    priority = 0
    string = 'upstream_gene_variant'

  [[regulatory_region_amplification]]
    score = 5
    priority = 1
    string = 'regulatory_region_amplification'

  [[tfbs_amplification]]
    score = 5
    priority = 1
    string = 'tfbs_amplification'

  [[5_prime_utr_variant]]
    score = 5
    priority = 1
    string = '5_prime_utr_variant'

  [[intron_variant]]
    score = 5
    priority = 1
    string = 'intron_variant'

  [[3_prime_utr_variant]]
    score = 5
    priority = 1
    string = '3_prime_utr_variant'

  [[feature_truncation]]
    score = 5
    priority = 1
    string = 'feature_truncation'

  [[TF_binding_site_variant]]
    score = 5
    priority = 1
    string = 'TF_binding_site_variant'

  [[stop_retained_variant]]
    score = 5
    priority = 1
    string = 'stop_retained_variant'

  [[feature_elongation]]
    score = 5
    priority = 1
    string = 'feature_elongation'

  [[regulatory_region_ablation]]
    score = 5
    priority = 1
    string = 'regulatory_region_ablation'

  [[tfbs_ablation]]
    score = 5
    priority = 1
    string = 'tfbs_ablation'

  [[coding_sequence_variant]]
    score = 5
    priority = 1
    string = 'coding_sequence_variant'

  [[downstream_gene_variant]]
    score = 0
    priority = 0
    string = 'downstream_gene_variant'

  [[NMD_transcript_variant]]
    score = 5
    priority = 1
    string = 'NMD_transcript_variant'

  [[intergenic_variant]]
    score = -5
    priority = 0
    string = 'intergenic_variant'

  [[not_reported]]
    score = 0
    
    
[OMIM]
  field = INFO
  data_type = string
  category = Consequence
  record_rule = max
  separators = '|'
  info_key = Omim
  description = reported Omim gene
  
  [[Found]]
    score = 5
    priority = 0
    string = 'Found'
    
  [[not_reported]]
    score = 0