Field description type properties example enum
alternateBases Alternate bases for this variant (starting from start). * Accepted values: IUPAC codes for nucleotides (e.g. https://www.bioinformatics.org/sms/iupac.html). N is a wildcard, that denotes the position of any base, and can beused as a standalone base of any type or within a partially knownsequence. As example, a query of ANNT the Ns can take take any form of[ACGT] and will match ANNT, ACNT, ACCT, ACGT ... and so forth. an empty value is used in the case of deletions with the maximally trimmed, deleted sequence being indicated in ReferenceBases Categorical variant queries, e.g. such not being represented through sequence & position, make use of the variantType parameter. * Either alternateBases or variantType is required. string NA NA NA
caseLevelData caseLevelData reports about the variation instances observed in individual analyses. array alleleOrigin, analysisId, biosampleId, clinicalInterpretations, id, individualId, phenotypicEffects, runId, zygosity NA NA
frequencyInPopulations NA array frequencies, source, sourceReference, version NA NA
identifiers NA object clinVarIds, genomicHGVSId, proteinHGVSIds, transcriptHGVSIds, variantAlternativeIds NA NA
molecularAttributes NA object aminoacidChanges, geneIds, genomicFeatures, molecularEffects NA NA
position This section groups all attributes that allows to identify a variant via its position in the genome. object assemblyId, end, refseqId, start NA NA
referenceBases Reference bases for this variant (starting from start). * Accepted values: IUPAC codes for nucleotides (e.g. https://www.bioinformatics.org/sms/iupac.html). N is a wildcard, that denotes the position of any base, and can be used as a standalone base of any type or within a partially known sequence. As example, a query of ANNT the Ns can take take any form of [ACGT] and will match ANNT, ACNT, ACCT, ACGT ... and so forth. * an empty value is used in the case of insertions with the maximally trimmed, inserted sequence being indicated in AlternateBases. NOTE: Many Beacon instances could not support UIPAC codes and it is not mandatory for them to do so. In such cases the use of [ACGTN] is mandated. string NA NA NA
variantInternalId Reference to the internal variant ID. This represents the primary key/identifier of that variant inside a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the identifiers section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the identifiers section. string NA NA NA
variantLevelData NA object clinicalInterpretations, phenotypicEffects NA NA
variantType The variantType declares the nature of the variation in relation to a reference. In a response, it is used to describe the variation. In a request, it is used to declare the type of event the Beacon client is looking for. If in queries variants can not be defined through a sequence of one or more bases (precise variants) it can be used standalone (i.e. without alternateBases) together with positional parameters. Examples here are e.g. queries for structural variants such as DUP (increased allelic count of material from the genomic region between start and end positions without assumption about the placement of the additional sequence) or DEL (deletion of sequence following start). Either alternateBases or variantType is required, with the exception of range queries (single start and end parameters). string NA SNP, DEL, DUP, BND NA