Illumina Annotation Service

Illumina Annotation Service (IAS) provided annotations are listed below.

ID

Description

INFO
• CSQT – Transcript consequence as predicted by Variant Effect Predictor (www.ensembl.org/info/docs/tools/vep/index.html) version 72. Only canonical transcripts are included in the VCF file to maintain readability. The ANT file contains consequences for all affected transcripts. This binary file can be loaded into VariantStudio for viewing; see www.illumina.com/clinical/clinical_informatics/illumina-variantstudio.ilmn.

A comma-separated list for each affected gene is provided. Each entry in the list includes the HGNC gene symbol (when available), transcript ID, and functional consequences in a delimited format: HGNC|TranscriptID|Consequence. If the annotation source selected was RefSeq, then many of the TranscriptIDs will begin with NM_. If the selected annotation source was Ensembl, then the TranscriptIDs begin with ENST. The consequences are indicated using valid Sequence Ontology (SO) terms (www.ensembl.org/info/genome/variation/predicted_data.html#consequences).

• CSQR – Regulatory consequence as predicted by Variant Effect Predictor (www.ensembl.org/info/docs/tools/vep/index.html) version 72. A comma-separated list for each affected regulatory region (including transcription factor binding sites) is provided using the following delimited format: RegulatoryID|Consequence. The annotations provided in this field come from the Ensembl database of regulatory features even if RefSeq was selected as the annotation source. Many of the RegulatoryIDs begin with ENSR. The consequences are indicated using valid Sequence Ontology (SO) terms (www.ensembl.org/info/genome/variation/predicted_data.html#consequences) and typically are either regulatory_region_variant or TF_binding_site_variant.
• AF – The allele frequency from all populations of 1000 genomes data
• AA – The inferred allele ancestral to the chimpanzee/human lineage
• GMAF – Global minor allele frequency (GMAF); technically, the frequency of the second most frequent allele. Format: GlobalMinorAllele|AlleleFreqGlobalMinor
• EVS – Allele frequency, sample count, and coverage taken from the Exome Variant Server (EVS). Format: AlleleFreqEVS|EVSCoverage|EVSSamples
• cosmic – The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database (cancer.sanger.ac.uk/cancergenome/projects/cosmic/).
• clinvar – Clinical significance from the ClinVar database (www.ncbi.nlm.nih.gov/clinvar/).
• phastCons – Denotes if the variant is an identical or similar sequence that occurs between species and maintained between species throughout evolution

 

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