Appendix 6. Opal Annotation Engine

Jeanette McCarthy -

Opal Annotation Engine is a comprehensive annotation pipeline that appends gene and impact information, multiple predictive scores, as well as links to literature evidence. It annotates all variants in the variant file. Annotations include synonymous, non-synonymous, slice site, stop gain/loss SNPs, small indels (25bp or less) that may induce frame-shifts, and regulatory regions. Variants within 5 Kb of a gene are annotated as up/downstream variants. Large structural or copy number variant annotations are not included at this time.

Opal Annotation Engine incorporates algorithms including VEP from Ensembl, SnpSift, Omicia Score Agent, and Omicia Evidence Agent, as well as data sources including dbSNP, dbNSFP and 1000 Genomes.

Opal Annotation Engine Variant Reports include all variants introns and intergenic regions. Modify the Exclude filters in Variant Miner to see the intronic and intergenic variants.

Annotated Biotypes and Genes

Opal Annotation Engine annotates the following Ensembl biotypes:


  • protein_coding
  • IG_C_gene
  • IG_D_gene
  • IG_J_gene
  • IG_V_gene
  • TR_C_gene
  • TR_D_gene
  • TR_J_gene
  • TR_V_gene


  • Mt_tRNA
  • Mt_rRNA
  • rRNA
  • processed_transcript
  • miRNA
Opal Annotation Engine also annotates all transcripts for the following genes, regardless of Ensembl biotype:
  • ACTN3
  • CASC16
  • CDKN2B-AS1
  • CYP2D7P 
  • DGCR5
  • GNAS-AS1
  • GPR33
  • KCNQ1OT1
  • MIAT
  • PTCSC3
  • PWRN1
  • RMRP
  • SNORD115-1
  • SNORD116-1
  • SNORD116-10
  • TAAR9
  • TERC
  • TTTY13
  • WT1-AS
  • XIST


Opal Pipeline 3 Reports

Variant Reports from Opal Pipeline 3 only show variants in introns or intergenic regions if they:



See Appendix 5 for details on annotation pipeline data source release versions.

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