WGS Variant Effect Predictor Fields

WGS Annotation VEP Fields

Once variant calling has completed for whole genome sequences (WGS), researchers want to know more about the variants, such as whether the variant impacts protein coding or how common the variant is in various populations.

AMP PD utilized tools from the Google Cloud Health team for its variant annotations. The table below details what databases and annotation fields were included in the VEP annotation pipeline.

Field	Type	Mode	Description
alternate_bases.CSQ	RECORD	REPEATED	List of CSQ annotations for this alternate.
alternate_bases.CSQ.allele	STRING	NULLABLE	The ALT part of the annotation field.
alternate_bases.CSQ.Consequence	STRING	NULLABLE	Consequence type of this variant
alternate_bases.CSQ.IMPACT	STRING	NULLABLE	The impact modifier for the consequence type
alternate_bases.CSQ.SYMBOL	STRING	NULLABLE	The gene symbol
alternate_bases.CSQ.Gene	STRING	NULLABLE	Ensembl stable ID of affected gene
alternate_bases.CSQ.Feature_type	STRING	NULLABLE	Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.
alternate_bases.CSQ.Feature	STRING	NULLABLE	Ensembl stable ID of feature
alternate_bases.CSQ.BIOTYPE	STRING	NULLABLE	Biotype of transcript or regulatory feature
alternate_bases.CSQ.EXON	STRING	NULLABLE	The exon number (out of total number)
alternate_bases.CSQ.INTRON	STRING	NULLABLE	The intron number (out of total number)
alternate_bases.CSQ.HGVSc	STRING	NULLABLE	The HGVS coding sequence name
alternate_bases.CSQ.HGVSp	STRING	NULLABLE	The HGVS protein sequence name
alternate_bases.CSQ.cDNA_position	STRING	NULLABLE	Relative position of base pair in cDNA sequence
alternate_bases.CSQ.CDS_position	STRING	NULLABLE	Relative position of base pair in coding sequence
alternate_bases.CSQ.Protein_position	STRING	NULLABLE	Relative position of amino acid in protein
alternate_bases.CSQ.Amino_acids	STRING	NULLABLE	Reference and variant amino acids. Only given if the variant affects the protein-coding sequence
alternate_bases.CSQ.Codons	STRING	NULLABLE	The alternative codons with the variant base in upper case
alternate_bases.CSQ.Existing_variation	STRING	NULLABLE	Known identifier of existing variant
alternate_bases.CSQ.ALLELE_NUM	STRING	NULLABLE	Allele number from input; 0 is reference, 1 is first alternate etc
alternate_bases.CSQ.DISTANCE	STRING	NULLABLE	Shortest distance from variant to transcript
alternate_bases.CSQ.STRAND	STRING	NULLABLE	The DNA strand (1 or -1) on which the transcript/feature lies
alternate_bases.CSQ.FLAGS	STRING	NULLABLE	Transcript quality flags (cds_start_NF, cds_start_NF)
alternate_bases.CSQ.VARIANT_CLASS	STRING	NULLABLE	Sequence Ontology variant class
alternate_bases.CSQ.SYMBOL_SOURCE	STRING	NULLABLE	The source of the gene symbol
alternate_bases.CSQ.HGNC_ID	STRING	NULLABLE	HUGO Gene Nomenclature Committee approved symbol
alternate_bases.CSQ.CANONICAL	STRING	NULLABLE	A flag indicating if the transcript is denoted as the canonical transcript for this gene
alternate_bases.CSQ.TSL	STRING	NULLABLE	Transcript support level. NB: not available for GRCh37
alternate_bases.CSQ.APPRIS	STRING	NULLABLE	Annotates alternatively spliced transcripts as primary or alternate based on a range of computational methods. NB: not available for GRCh37
alternate_bases.CSQ.CCDS	STRING	NULLABLE	The CCDS identifer for this transcript, where applicable
alternate_bases.CSQ.ENSP	STRING	NULLABLE	The Ensembl protein identifier of the affected transcript
alternate_bases.CSQ.SWISSPROT	STRING	NULLABLE	Best match UniProtKB/Swiss-Prot accession of protein product
alternate_bases.CSQ.TREMBL	STRING	NULLABLE	Best match UniProtKB/TrEMBL accession of protein product
alternate_bases.CSQ.UNIPARC	STRING	NULLABLE	Best match UniParc accession of protein product
alternate_bases.CSQ.GENE_PHENO	STRING	NULLABLE	Indicates if overlapped gene is associated with a phenotype, disease or trait
alternate_bases.CSQ.SIFT	STRING	NULLABLE	The SIFT prediction and/or score, with both given as prediction(score)
alternate_bases.CSQ.PolyPhen	STRING	NULLABLE	The PolyPhen prediction and/or score
alternate_bases.CSQ.DOMAINS	STRING	NULLABLE	The source and identifer of any overlapping protein domains
alternate_bases.CSQ.HGVS_OFFSET	STRING	NULLABLE	Indicates by how many bases the HGVS notations for this variant have been shifted
alternate_bases.CSQ.AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes
alternate_bases.CSQ.AFR_AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes combined African population
alternate_bases.CSQ.AMR_AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes combined American population
alternate_bases.CSQ.EAS_AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes combined East Asian population
alternate_bases.CSQ.EUR_AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes combined European population
alternate_bases.CSQ.SAS_AF	STRING	NULLABLE	Frequency of existing variant in 1000 Genomes combined South Asian population
alternate_bases.CSQ.AA_AF	STRING	NULLABLE	Frequency of existing variant in NHLBI-ESP African American population
alternate_bases.CSQ.EA_AF	STRING	NULLABLE	Frequency of existing variant in NHLBI-ESP European American population
alternate_bases.CSQ.gnomAD_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes combined population
alternate_bases.CSQ.gnomAD_AFR_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes African/American population
alternate_bases.CSQ.gnomAD_AMR_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes American population
alternate_bases.CSQ.gnomAD_ASJ_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes Ashkenazi Jewish population
alternate_bases.CSQ.gnomAD_EAS_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes East Asian population
alternate_bases.CSQ.gnomAD_FIN_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes Finnish population
alternate_bases.CSQ.gnomAD_NFE_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes Non-Finnish European population
alternate_bases.CSQ.gnomAD_OTH_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes combined other combined populations
alternate_bases.CSQ.gnomAD_SAS_AF	STRING	NULLABLE	Frequency of existing variant in gnomAD exomes South Asian population
alternate_bases.CSQ.MAX_AF	STRING	NULLABLE	Maximum observed allele frequency in 1000 Genomes, ESP and gnomAD
alternate_bases.CSQ.MAX_AF_POPS	STRING	NULLABLE	Populations in which maximum allele frequency was observed
alternate_bases.CSQ.CLIN_SIG	STRING	NULLABLE	ClinVar clinical significance of the dbSNP variant
alternate_bases.CSQ.SOMATIC	STRING	NULLABLE	Somatic status of existing variant(s); multiple values correspond to multiple values in the Existing_variation field
alternate_bases.CSQ.PHENO	STRING	NULLABLE	Indicates if existing variant is associated with a phenotype, disease or trait; multiple values correspond to multiple values in the Existing_variation field
alternate_bases.CSQ.PUBMED	STRING	NULLABLE	Pubmed ID(s) of publications that cite existing variant
alternate_bases.CSQ.MOTIF_NAME	STRING	NULLABLE	The source and identifier of a transcription factor binding profile aligned at this position
alternate_bases.CSQ.MOTIF_POS	STRING	NULLABLE	The relative position of the variation in the aligned TFBP
alternate_bases.CSQ.HIGH_INF_POS	STRING	NULLABLE	A flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP)
alternate_bases.CSQ.MOTIF_SCORE_CHANGE	STRING	NULLABLE	The difference in motif score of the reference and variant sequences for the TFBP