Annotate variants

The Annotate variants report builder annotates variants from a set of subjects with VEP summary information, gene-disease information, gene ontology codes, paralogs, etc.

The dialog generates a table of variant and gene annotations for variants meeting user defined criteria in subjects. The annotation may also be limited to variants within a set of genes of interest or within a specific genomic range.

The following annotations are added to each variant in addition to ACMG category scores:

• Gene annotation from the Clinical Genome Database (CGD)

• Gene annotation from European Commission project database

• Gene biotype, gene ID, gene related pathway, gene parlous etc.

• GO term ID and description

• Genotype of each variant, call copies, call ratios, read depth, etc.

• Information from public databases, such as related diseases, gene related diseases, variant related diseases, etc.

• OMIM annotation of each related gene

• VEP annotation of each variant, such as max_consequence, max_impact, max_score etc.

Annotate Variants in Sequence Miner

Example use case

The user wishes to annotate variants in selected subjects that meet user-defined criteria with information such as pathways, paralogs, known diseases involving each gene and clinically relevant information (from the CGD). The user also wants to identify heterozygous and homozygous variants in the subject(s).

Description of the algorithm

This query creates a table of variants for each input subject (PN) that meet the user’s filtering criteria (e.g., call quality, maximum impact, consequence and allele frequency of the variant). The table is then joined to annotation tables.

Variants are annotated with CAT scores. The DIAG ACMG CAT scores are calculated as follows:

• If the AF > the user’s designated maxAF threshold (e.g., maxAF>0.01), then the variant is CAT4.

• If the variant is not CAT4 and if MaxClinImpact is “pathogenic” (in the ref/clinical_variants.gorz file), then the variant is CAT1.

• If the variant is neither CAT4 or CAT1 and the max_impact is “HIGH” (from the source/anno/vep_v3-4-2/vep_single_wes.gord file), then the variant is CAT2.

• If the variant is neither CAT1, 2 or 4 and

• if max_Consequence = “missense_variant” and max_score >= 0.9, the variant is CAT3A

OR

• If max_impact = “LOW” or (max_impact = “MODERATE” and Cat3A = 0), the variant is CAT3B

Interpreting the output

The output table includes multiple annotation columns which are grouped by category and can be viewed in either the Default view or AMCG Perspective views. Output columns and perspectives are described below.

Column descriptions

Basic columns and descriptions

Group	Column	Description
Basic
	Call	The actual called sequence (variant), found by replacing a part of the reference sequence and denoted by Pos and Reference, with the sequence in the Call column
	Chrom	The chromosome of the variant represented as chr1, chr2, …, chr22, chrXY, chrX, chrY, chrM
	hetORhom	The zygosity of the call, either “het” or “hom”
	PN	The patient number (identifier)
	Pos	The (first) base pair position of the sequence variant, i.e., the position of the first nucleotide in the Reference column
	Reference	Sequence from the reference build, the first base starting at the base pair position in the Pos column

CGD columns and descriptions

Group	Column	Description
CGD		The CGD (Clinical Genome Database) columns provide information for variants based on the manually curated database of variants associated with known clinically significant conditions and available interventions.
	AGE_GROUP	Pediatric: less than 18 years of age; Adult: at least 18 years of age
	COMMENTS	Any additional observations noted by curators
	CONDITION	Conditions also resulting from mutations in the same gene but may otherwise be placed in the “General” Intervention category
	INHERITANCE	Pattern of inheritance the variant is known to follow: AD - autosomal dominant; AR - autosomal recessive; BG - blood group; Digenic - a condition resulting from simultaneous mutations in different genes; Maternal - maternal mitochondrial inheritance; XL - X-linked (because X-linked conditions can frequently have manifestations in both genetic sexes, X-linked conditions are not designated as dominant or recessive)
	INTERVENTION CATEGORIES	This category includes organ systems for which specific and additional inteventions may be beneficial
	INTERVENTION RATIONALE	Description of the intervention and its benefit
	MANIFESTATION CATEGORIES	This category includes organ systems affected by mutations in corresponding genes; recognition of involved organ systems may help guide supportive care
	REFERENCES	CGD: Clinical Genomic Database by NHGRI; PubMed ID of the reference from which the information was taken

COMM columns and descriptions

Group	Column	Description
COMM		The COMM columns provide variant annotation (comments) added to CSA or Sequence Miner by users
	CLINICAL_SIGNIFICANCE	The clinical significance (e.g., pathogenic, benign, unknown significance, drug-response, risk factor, etc.) of the variant as annotated (commented) by users; if the same variant has several comments, this cell will contain a set of values
	MODE_OF_INHERITANCE	The user-annotated (commented) mode of inheritance of the variant; if the same variant has several comments, this cell will contain a set of values
	TEXT	The description (comment) component for the user annotation of the variant

EuroGenetest columns and descriptions

Group	Column	Description
EuroGenetest		The EuroGenetest columns are derived from a European Commission project database containing European genetic testing information for particular genes, variants, and diseases.
	Diseases	Diseases associated with a variant derived from the European Commission project database
	NoOfDiseases	Number of diseases associated with a variant derived from the European Commission project database
	NoOfpanels	Number of gene panels associated with a variant derived from the European Commission project database
	panels	EuroGenetest panels associated with a variant derived from the European Commission project database

Gene columns and descriptions

Group	Column	Description
Gene		The Gene columns provide information based on the candidate gene in which a variant is found. When possible, the HUGO Gene Nomenclature Committee (HGNC) gene symbol is provided. Columns list gene annotations for the variants identified, including gene biotype, gene ID, gene related pathway, gene paralogs, etc.
	Aliases	The aliases of the given gene
	Biotype	Biological class of gene as annotated by VEP
	cdsEnd	cDNA end position as annotated by VEP
	cdsStart	cDNA start position as annotated by VEP
	Description	Description of the gene, i.e., full gene name
	gene_stable_id	Ensembl stable ID for the gene
	Paralogs	The paralogs of the given gene
	Pathways	The pathway(s) in which a given gene is found and listed in Ensembl in the ref/ensgenes/ensgenes_gene2pathway.mmap file
	Strand	The transcription strand for the gene (+/-)
	Symbol	Based on HGNC when it exists, otherwise it is the Ensembl internal alias

GO columns and descriptions

Group	Column	Description
GO		The GO columns provide a functional annotation of the gene product in which the variant is found. Columns list Gene Ontology (GO) annotations for the gene, including the GO term ID and term description.
	Descriptions	Gene ontology category descriptions
	IDs	Gene ontology identifiers

GT columns and descriptions

Group	Column	Description
GT		The GT (genotype) columns provide quality control information for the variant call based on the sequence read depth and quality. These scores are based on the Genome Analysis Toolkit (GATK) measures. Columns list genotype information derived from the VCF, including the variant call, call copies, call ratio, call quality, and read depth.
	CallCopies	Because the focus is only on variations from the reference, CallCopies refer to how many copies of the variation exist in a subject. A CallCopies value of “2” therefore corresponds to a homozygous variant, whereas a CallCopies value of “1” corresponds to a heterozygous variation.
	CallRatio	Proportion of reads containing the variant call; expected to be close to 0.5 for heterozygous calls and close to 1 for homozygous calls
	Depth	The number of reads covering the variant call
	FILTER	Quality parameter using the ratio between gt-quality and depth showing if the call is considered LowQual quality (not useable) or PASS; this remains a crude quality measure
	GL_Call	A statistical measure indicating the likelihood that the call is wrong; the scale has been converted to use only integers - the higher the number, the less likely it is that the call is wrong

KNOWN columns and descriptions

Group	Column	Description
KNOWN		The KNOWN columns provide publicly available information about the candidate gene and/or variant as annotated by ClinVar, HGMD, and OMIM. Columns list publicly known clinical annotations derived from ClinVar, OMIM, and HGMD Professional for the variant and gene including related diseases and predicted clinical impact.
	gene_diseases	Diseases known to be associated with the gene as annotated in ClinVar, HGMD, and OMIM
	gene_lists	Gene list membership of the gene in which the variant is found in the ref/ensgenes/ensgenes_disease.map file.
	InACMG	A Boolean column (“true” or “false”) indicating whether the gene is in the ACMG recommended list of genes for incidental findings and reporting
	var_diseases	Diseases known to be associated with the variant as annotated by ClinVar, HGMD, and OMIM

OMIM columns and descriptions

Group	Column	Description
OMIM		The OMIM columns provide the OMIM-designated identification for a particular gene and related disease description.
	Descriptions	OMIM disease descriptions for the gene
	IDs	The OMIM ID of the gene

VEP columns and descriptions

Group	Column	Description
VEP		The VEP columns provide functional annotations for variants based on the ENSEMBL SNP Effect Predictor database. Columns list Variant Effect Predictor (VEP) annotation for each variant, including the max_consequence, max_impact, max_score, and transcript information.
	Amino_Acids	The amino acid with and without variant, separated by a “/” (provided only if the variant affects the protein-coding sequence), otherwise “.”
	max_consequence	Consequence type reported for this variant having the greatest impact
	Max_Impact	Classification of the level of severity of the transcript consequence type assigned by VEP
	Max_Score	Maximum score for the variant as observed in dbNSFP [Score=max ((1-Sift_score), Polyphen2_HDIV_score, Polyphen2_HVAR_score)]
	Protein_Position	Position of the amino acid in the protein sequence (only if the variant falls within a coding sequence); a value is given for each corresponding transcript specified in the CDS position field

Other columns and descriptions

Group	Column	Description
Other columns
	dbSNP_rsIDs	The dbSNP identifier
	DIAG_ACMGCat	Categorization of the sequence variants according to the ACMG scheme
	formatZip	VCF genotype fields
	FS	Fisher’s exact test of read strand. If the reference reads are balanced between forward and reverse strands then the alternate reads should be as well
	max_af	Maximum reported allele frequency (1000GP3, EVS, EXAC, Kyoto, GONL)

Perspective views

Perspectives subtabs focus on subsets of the columns in the Default view.

Perspectives

Perspective	Description
ACMG	Displays only CAT 1 and 2 variants that are Known InACMG (“True”). The following annotation columns are displayed in this perspective: DIAG_ACMGCat, max_consequence, KNOWN_Gene_diseases, and KNOWN_var diseases.
Default view	Displays all columns