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In the Most Frequent Mutations table for the VEP impact score, which algorithm in the VEP is the GDC using to determine “H" or “M”?

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The IMPACT is categorized by the Sequencing Ontology type of the variants that is also compatible to snpEff. The VEP IMPACT rating is a separate rating given for compatibility with other variant annotation tools (e.g. snpEff). Basically, each category is associated with a set of SO terms:

  • HIGH: The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay: transcript_ablation, splice_acceptor_variant, splice_donor_variant, stop_gained, frameshift_variant, stop_lost, start_lost, transcript_amplification
  • MODERATE: A non-disruptive variant that might change protein effectiveness: inframe_insertion, inframe_deletion, missense_variant, protein_altering_variant, regulatory_region_ablation
  • LOW: Assumed to be mostly harmless or unlikely to change protein behavior: splice_region_variant, incomplete_terminal_codon_variant, stop_retained_variant, synonymous_variant
  • MODIFIER: Usually non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact: coding_sequence_variant, mature_miRNA_variant, 5_prime_UTR_variant, 3_prime_UTR_variant, non_coding_transcript_exon_variant, intron_variant, NMD_transcript_variant, non_coding_transcript_variant, upstream_gene_variant, downstream_gene_variant, TFBS_ablation, TFBS_amplification, TF_binding_site_variant, regulatory_region_amplification, feature_elongation, regulatory_region_variant, feature_truncation, intergenic_variant

Details about predicted data in variations are available at ENSEMBL

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