docs: def count_missense_per_gene(lines):
      """ count the number of missense variants in each gene.
      """
      
      counts = {}
      for x in lines:
          x = x.split("\t")
          gene = x[0]
          consequence = x[3]
          
          if gene not in counts:
              counts[gene] = 0
          
          if consequence != "missense_variant":
              continue
          
          counts[gene] += 1
      
      return counts