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Table 4 Variant annotators comparison for a tRNA gene mutation

From: A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs

MToolBox Annotation Example
 Locus MT-TM
 rCRS Yes
 Other Haplogroups  
 Nt Variability 0.00E+00
 tRNA Annotation 53;II;TS;G;N
 Patho-prediction RNA coding genes 0.65
 MITOMAP Associated Disease(s) Myopathy
 MITOMAP Homoplasmy N
 MITOMAP Heteroplasmy Y
 PhastCons20Way 0.889764
 PhyloP20Way 0.797921
SnpEff Annotation Example
 Annotation non_coding_exon_variant
 Annotation_Impact MODIFIER
 Gene_Name MT-TM
 Gene_ID ENSG00000210112
 Feature_Type Transcript
 Feature_ID ENST00000387377
 Transcript_BioType Mt_tRNA
 Rank 1/1
 HGVS.c n.49G>A
MitoBamAnnotator Example
 pos 4450
 ref G
 from G
 to A
 gene MT-TM
 coding for tRNA
 coding region 0
 is mutated 1
 triplet position NA
 mutation type NA
 has_overlap 0
mit-o-matic Example
 Variant 4450
 Ref allele G
 Alt allele A
 Gene MT-TM
 Disease Myopathy
  1. Among tools providing annotations for a specific variant in a tRNA gene (m.4450G>A) chosen for its potential damaging effect, MToolBox showed the widest range of useful features provided in the final annotation step allowing users to prioritize the variant. Empty fields were omitted. Tested tools which do not provide annotations for tRNA variants were not reported