API Response Fields

This page describes all fields returned by the variant annotation API. The root object contains a list of variants and an optional message.

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You can see API in action by clicking an API link on any variant on GeneBe website or you can try this API Showcase

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Top-level fields

Field	Description
variants	List of variant annotation objects.
message	Informational message or error text, if applicable.

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Variant fields (variants[])

Field	Description
chr	Chromosome where the variant occurs (e.g. "6"), "M" for mitochondrium
pos	Genomic position of the variant (1-based coordinate). Just like in a VCF file.
ref	Reference allele in the reference genome. Just like in a VCF file.
alt	Alternate allele observed in the sample. Just like in a VCF file.
effect	Main predicted functional effect (e.g. "missense_variant"). This is the main chosen effect in the main chosen transcript in the main chosen gene.
transcript	Reference transcript used for top-level annotation (RefSeq ID or Ensembl ID). System chooses wisely which transcript should be used in case of many transcripts / genes in the region of interest.
gene_symbol	Gene symbol associated with the variant (e.g. "LPA"). If in the region of interest are many genes: algorithm chooses one.
gene_hgnc_id	HGNC gene identifier of the gene from the gene_symbol.
dbsnp	dbSNP identifier (e.g. "rs41272110").
frequency_reference_population	Allele frequency of the variant in the current available database of healthy individuals (population database). At the moment of writing gnomAD Total (Exome + Genome), version 4.1 is used, but this will change in the future if better alternatives appears.
hom_count_reference_population	Number of homozygotes in the population database.
allele_count_reference_population	Number of allele counts with this variant in the population database.
gnomad_exomes_af	Allele frequency in gnomAD exome dataset.
gnomad_genomes_af	Allele frequency in gnomAD genome dataset.
gnomad_exomes_ac	Allele count in gnomAD exome dataset.
gnomad_genomes_ac	Allele count in gnomAD genome dataset.
gnomad_exomes_homalt	Number of homozygous alternate individuals in gnomAD exomes.
gnomad_genomes_homalt	Number of homozygous alternate individuals in gnomAD genomes.
gnomad_mito_homoplasmic	Number of individuals in gnomAD with this variant on mitochondrium with VAF suggesting being homoplasmic
gnomad_mito_heteroplasmic	Number of individuals in gnomAD with this variant on mitochondrium with VAF suggesting being heteroplasmic
computational_score_selected	Score from the selected computational pathogenicity predictor.
computational_prediction_selected	Verdict from the selected computational predictor (e.g. “Benign”, “Damaging”).
computational_source_selected	Name of the computational model used (e.g. "MetaRNN").
splice_score_selected	Splice prediction score (selected model).
splice_prediction_selected	Splice effect prediction (“Benign”, “Damaging”, etc.).
splice_source_selected	Source model for the splice prediction (e.g. "max_spliceai").
revel_score	REVEL ensemble score for missense variants.
revel_prediction	Interpretation of the REVEL score.
alphamissense_score	AlphaMissense predicted score.
alphamissense_prediction	AlphaMissense verdict (“Benign”, “Pathogenic”, etc.).
bayesdelnoaf_score	BayesDel-noAF score.
bayesdelnoaf_prediction	BayesDel-noAF prediction verdict.
phylop100way_score	PhyloP 100-way evolutionary conservation score.
phylop100way_prediction	Interpretation of the PhyloP conservation score.
spliceai_max_score	Maximum SpliceAI score across all four positions.
spliceai_max_prediction	Interpretation of the SpliceAI result.
dbscsnv_ada_score	dbscSNV ADA score for splice site alteration.
dbscsnv_ada_prediction	dbscSNV ADA prediction verdict.
apogee2_score	APOGEE2 mitochondrial variant score.
apogee2_prediction	APOGEE2 prediction verdict.
mitotip_score	MitoTIP tRNA variant score.
mitotip_prediction	MitoTIP verdict.
acmg_score	Aggregate ACMG score (computed rule-based classification).
acmg_classification	Final ACMG verdict (“Benign”, “Pathogenic”, etc.).
acmg_criteria	Applied ACMG criteria codes (comma-separated).
acmg_by_gene	Gene-specific ACMG evidence and scoring. See below.
clinvar_disease	ClinVar disease name(s).
clinvar_classification	ClinVar pathogenicity classification.
clinvar_review_status	ClinVar review confidence level.
clinvar_submissions_summary	Summary of ClinVar submitters’ evaluations.
phenotype_combined	Phenotype combined from multiple sources
pathogenicity_classification_combined	Pathogenicity classification combined from multiple sources
custom_annotations	For future use
consequences	List of per-transcript consequence annotations. See below.

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Consequence fields (variants.consequences[])

Field	Description
aa_ref	Reference amino acid.
aa_alt	Alternate amino acid.
canonical	Whether this transcript is the canonical one for the gene.
protein_coding	Whether the transcript encodes a protein.
strand	DNA strand of the transcript (true = forward, false = reverse).
consequences	List of sequence ontology consequence terms.
exon_rank	Rank (index) of the exon where the variant occurs.
exon_count	Total number of exons in the transcript.
gene_symbol	Gene symbol associated with the transcript.
gene_hgnc_id	HGNC identifier for the gene.
hgvs_c	HGVS coding DNA-level description (e.g. "c.4195A>C").
hgvs_p	HGVS protein-level description (e.g. "p.Thr1399Pro").
transcript	Transcript accession (RefSeq or Ensembl).
protein_id	Protein accession corresponding to the transcript.
transcript_support_level	Ensembl Transcript Support Level (1 = best).
aa_start	Amino acid position where the change starts.
aa_length	Total amino acid length of the protein.
cds_start	Position of the coding sequence change.
cdna_start	Position of the change in cDNA coordinates.
mane_select	MANE Select transcript ID corresponding to this transcript.
mane_plus	MANE Plus Clinical transcript ID, if available.
biotype	For example protein_coding
feature	To be used when we start annotating with regions: the ID of the functional region

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ACMG-by-gene fields (variants.acmg_by_gene[])

Field	Description
score	Overall ACMG gene-specific score.
benign_score	Total benign evidence contribution.
pathogenic_score	Total pathogenic evidence contribution.
criteria	List of ACMG criteria applied (e.g. "BP4_Strong", "BA1").
verdict	Final classification (“Benign”, “Likely pathogenic”, etc.).
transcript	Transcript used for the ACMG assessment.
gene_symbol	Gene symbol.
hgnc_id	HGNC gene ID.
effects	Consequence terms related to this gene.
inheritance_mode	Inheritance mode considered (e.g. "AR", "AD").
hgvs_c	Coding HGVS notation for this transcript.
hgvs_p	Protein HGVS notation for this transcript.

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