openapi: 3.1.0 info: title: annonars description: Genome annotation based on Rust and RocksDB contact: name: Manuel Holtgrewe email: manuel.holtgrewe@bih-charite.de license: name: Apache-2.0 version: 0.42.0 paths: /api/v1/genes/clinvar: get: tags: - genes_clinvar summary: Query for ClinVar information for one or more genes. operationId: genesClinvar parameters: - name: hgnc_id in: query description: The HGNC IDs to search for. required: false schema: type: - array - 'null' items: type: string responses: '200': description: Per-gene ClinVar information. content: application/json: schema: $ref: '#/components/schemas/GenesClinvarResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/genes/info: get: tags: - genes_info summary: Query for annotations for one or more genes. operationId: genesInfo parameters: - name: hgnc_id in: query description: The HGNC IDs to search for. required: false schema: type: - array - 'null' items: type: string responses: '200': description: Per-gene information. content: application/json: schema: $ref: '#/components/schemas/GenesInfoResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/genes/lookup: get: tags: - genes_lookup summary: Search for genes. operationId: genesLookup parameters: - name: q in: query description: The strings to search for. required: true schema: type: array items: type: string responses: '200': description: Genes search results. content: application/json: schema: $ref: '#/components/schemas/GenesLookupResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/genes/search: get: tags: - genes_search summary: Search for genes. operationId: genesSearch parameters: - name: q in: query description: The string to search for. required: true schema: type: string - name: fields in: query description: The fields to search in. required: false schema: type: - array - 'null' items: $ref: '#/components/schemas/GenesFields' - name: case_sensitive in: query description: Enable case sensitive search. required: false schema: type: - boolean - 'null' responses: '200': description: Genes search results. content: application/json: schema: $ref: '#/components/schemas/GenesSearchResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/seqvars/annos: get: tags: - annos_variant summary: Query for annotations for a single variant. operationId: seqvarsAnnosQuery parameters: - name: genome_release in: query description: Genome release specification. required: true schema: type: string - name: chromosome in: query description: Chromosome name. required: true schema: type: string - name: pos in: query description: 1-based position for VCF-style variant. required: true schema: type: integer format: int32 minimum: 0 - name: reference in: query description: Reference allele bases. required: true schema: type: string - name: alternative in: query description: Alterantive allele bases. required: true schema: type: string responses: '200': description: Annotation for a single variant. content: application/json: schema: $ref: '#/components/schemas/SeqvarsAnnosResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/strucvars/clinvar/query: get: tags: - clinvar_sv summary: Endpoint for querying ClinVar SV annotations. operationId: strucvarsClinvarQuery parameters: - name: genome_release in: query description: Genome release specification. required: true schema: $ref: '#/components/schemas/GenomeRelease' - name: chromosome in: query description: Chromosome name. required: true schema: type: string - name: start in: query description: 1-based start position. required: true schema: type: integer format: int32 minimum: 0 - name: stop in: query description: 1-based stop postion. required: true schema: type: integer format: int32 minimum: 0 - name: variation_types in: query description: Optionally, the variant types. required: false schema: type: - array - 'null' items: $ref: '#/components/schemas/ClinvarExtractedVariationType' - name: min_overlap in: query description: Optionally, minimal overlap. required: false schema: type: - number - 'null' format: double - name: page_no in: query description: Optional 1-based page number. required: false schema: type: - integer - 'null' format: int32 minimum: 0 - name: page_size in: query description: Optional page size. required: false schema: type: - integer - 'null' format: int32 minimum: 0 responses: '200': description: Clinvar strucvars information. content: application/json: schema: $ref: '#/components/schemas/StrucvarsClinvarResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' /api/v1/versionsInfo: get: tags: - versions summary: Query for annotations for one variant. operationId: versionsInfo parameters: [] responses: '200': description: Version information. content: application/json: schema: $ref: '#/components/schemas/VersionsInfoResponse' '500': description: Internal server error. content: application/json: schema: $ref: '#/components/schemas/CustomError' components: schemas: AnnoDb: type: string description: Encode annotation database. enum: - other - cadd - dbsnp - dbnsfp - dbscsnv - gnomad_mtdna - gnomad_exomes - gnomad_genomes - helixmtdb - ucsc_conservation - clinvar ClinvarAccession: type: object description: Local type for `ClinVarAccession` required: - accession - version properties: accession: type: string description: Accession. version: type: integer format: int32 description: Version. submitter_identifiers: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSubmitterIdentifiers' description: The submitter's identifier. date_updated: type: - string - 'null' format: date-time description: |- The date that the latest update to the submitted record (SCV) became public in ClinVar. date_created: type: - string - 'null' format: date-time description: |- DateCreated is the date when the record first became public in ClinVar. ClinvarAffectedStatus: type: string description: Local enumeration for the affected status. enum: - yes - no - not_provided - unknown - not_applicable ClinvarAge: type: object description: Local type for an age. required: - value - unit - type properties: value: type: integer format: int32 description: The age value. unit: $ref: '#/components/schemas/ClinvarAgeUnit' description: The age unit. type: $ref: '#/components/schemas/ClinvarAgeType' description: The age type. ClinvarAgeType: type: string description: Local enumeration for an age type. enum: - minimum - maximum - single ClinvarAgeUnit: type: string description: Local enumeration for an age unit. enum: - days - weeks - months - years - weeks_gestation - months_gestation ClinvarAggregateClassificationSet: type: object description: |- Used to bundle different types of Classifications (germline, oncogenic, somatic clinical impact) ; Supports summary as well as submission details. NB: called "typeAggregateClassificationSet" in XSD. properties: germline_classification: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregatedGermlineClassification' description: The aggregate germline classification. somatic_clinical_impact: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregatedSomaticClinicalImpact' description: The aggregate somatic clinical impact. oncogenicity_classification: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregatedOncogenicityClassification' description: The aggregate oncogenicity classification. ClinvarAggregateGermlineReviewStatus: type: string description: Enumeration describing aggregate germline review status value. enum: - no_classification_provided - no_assertion_criteria_provided - criteria_provided_single_submitter - criteria_provided_multiple_submitters_no_conflicts - criteria_provided_conflicting_classifications - reviewed_by_expert_panel - practice_guideline - no_classifications_from_unflagged_records - no_classification_for_the_single_variant ClinvarAggregateOncogenicityReviewStatus: type: string description: Enumeration describing aggregate oncogenicity review status value. enum: - no_classification_provided - no_assertion_criteria_provided - criteria_provided_single_submitter - criteria_provided_multiple_submitters_no_conflicts - criteria_provided_conflicting_classifications - reviewed_by_expert_panel - practice_guideline - no_classifications_from_unflagged_records - no_classification_for_the_single_variant ClinvarAggregateSomaticClinicalImpactReviewStatus: type: string description: Enumeration describing aggregate somatic clinical impact review status value. enum: - no_classification_provided - no_assertion_criteria_provided - criteria_provided_single_submitter - criteria_provided_multiple_submitters - reviewed_by_expert_panel - practice_guideline - no_classifications_from_unflagged_records - no_classification_for_the_single_variant ClinvarAggregatedGermlineClassification: type: object description: |- Aggregated germline classification info. Corresponds to ``typeAggregatedGermlineClassification`` in XSD. nested elements required: - review_status - xrefs - citations - comments - history_records - conditions properties: review_status: $ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus' description: |- The aggregate review status based on all germline submissions for this record. description: type: - string - 'null' description: | We are not providing an enumeration for the values we report for germline classification within the xsd. Details are in explanation: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: |- Explanation is used only when the description is 'conflicting data from submitters' The element summarizes the conflict. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. history_records: type: array items: $ref: '#/components/schemas/ClinvarDescriptionHistory' description: History information. conditions: type: array items: $ref: '#/components/schemas/ClinvarTraitSet' description: List of conditions. date_last_evaluated: type: - string - 'null' format: date-time description: Date of last evaluation. date_created: type: - string - 'null' format: date-time description: Date of creation. most_recent_submission: type: - string - 'null' format: date-time description: Date of most recent submission. number_of_submitters: type: - integer - 'null' format: int32 description: Number of submitters. number_of_submissions: type: - integer - 'null' format: int32 description: Number of submissions. ClinvarAggregatedOncogenicityClassification: type: object description: |- Aggregated oncogenicity classification info. nested elements required: - review_status - xrefs - citations - comments - history_records - conditions properties: review_status: $ref: '#/components/schemas/ClinvarAggregateOncogenicityReviewStatus' description: |- The aggregate review status based on all somatic clinical impact submissions for this record. description: type: - string - 'null' description: |- We are not providing an enumeration for the values we report for somatic clinical impact classification within the xsd. Details are in xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. history_records: type: array items: $ref: '#/components/schemas/ClinvarDescriptionHistory' description: History information. conditions: type: array items: $ref: '#/components/schemas/ClinvarTraitSet' description: List of conditions. date_last_evaluated: type: - string - 'null' format: date-time description: Date of last evaluation. date_created: type: - string - 'null' format: date-time description: Date of creation. most_recent_submission: type: - string - 'null' format: date-time description: Date of most recent submission. number_of_submitters: type: - integer - 'null' format: int32 description: Number of submitters. number_of_submissions: type: - integer - 'null' format: int32 description: Number of submissions. ClinvarAggregatedSomaticClinicalImpact: type: object description: |- Aggregated somatic clinical impact info. nested elements required: - review_status - xrefs - citations - comments - history_records - conditions properties: review_status: $ref: '#/components/schemas/ClinvarAggregateSomaticClinicalImpactReviewStatus' description: |- The aggregate review status based on all somatic clinical impact submissions for this record. description: type: - string - 'null' description: |- We are not providing an enumeration for the values we report for somatic clinical impact classification within the xsd. Details are in xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. history_records: type: array items: $ref: '#/components/schemas/ClinvarDescriptionHistory' description: History information. conditions: type: array items: $ref: '#/components/schemas/ClinvarTraitSet' description: List of conditions. date_last_evaluated: type: - string - 'null' format: date-time description: Date of last evaluation. date_created: type: - string - 'null' format: date-time description: Date of creation. most_recent_submission: type: - string - 'null' format: date-time description: Date of most recent submission. number_of_submitters: type: - integer - 'null' format: int32 description: Number of submitters. number_of_submissions: type: - integer - 'null' format: int32 description: Number of submissions. ClinvarAllele: type: object description: |- This is a record per variant (Measure/@ID,AlleleID). Corresponds to "typeAllele" in XSD. required: - genes - name - variant_types - locations - other_names - protein_changes - hgvs_expressions - xrefs - comments - functional_consequences - allele_frequencies - allele_id - variation_id properties: genes: type: array items: $ref: '#/components/schemas/ClinvarAlleleGene' description: Gene list. name: type: string description: Name. canonical_spdi: type: - string - 'null' description: Canonical SPDI. variant_types: type: array items: type: string description: Variant type(s). locations: type: array items: $ref: '#/components/schemas/ClinvarLocation' description: Location. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: List of other names. protein_changes: type: array items: type: string description: These are the single-letter representations of the protein change. hgvs_expressions: type: array items: $ref: '#/components/schemas/ClinvarHgvsExpression' description: List of HGVS expressions. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Aggregated classifications. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: List of functional consequences. allele_frequencies: type: array items: $ref: '#/components/schemas/ClinvarAlleleFrequency' description: Allele frequencies. global_minor_allele_frequency: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGlobalMinorAlleleFrequency' description: Global minor allele frequencies. allele_id: type: integer format: int64 description: Allele ID. variation_id: type: integer format: int64 description: Variation ID. ClinvarAlleleDescription: type: object description: |- This is to be used within co-occurrence set. Corresponds to `typeAlleleDescr` in XSD. required: - name properties: name: type: string description: The name of the allele. relative_orientation: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRelativeOrientation' description: |- Optional relative orientation. NB: Unused in XML zygosity: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarZygosity' description: Optional zygosity. clinical_significance: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarClinicalSignificance' description: |- Optional clinical significance. Corresponds to `ClinicalSignificanceType` in XSD. ClinvarAlleleFrequency: type: object description: Local type for allele frequency. required: - value - source properties: value: type: number format: double description: Value. source: type: string description: Source. url: type: - string - 'null' description: URL. ClinvarAlleleGene: type: object description: |- Local type for Gene. nested elements required: - locations - omims - properties - full_name - gene_id - source properties: locations: type: array items: $ref: '#/components/schemas/ClinvarLocation' description: Gene's locations. omims: type: array items: type: integer format: int64 minimum: 0 description: OMIM ID. haploinsufficiency: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarDosageSensitivity' description: Haploinsuffiency. triplosensitivity: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarDosageSensitivity' description: Triplosensitivity. properties: type: array items: type: string description: |- Used to set key words for retrieval or display about a gene, such as genes listed by the ACMG guidelines. symbol: type: - string - 'null' description: Optional gene symbol. full_name: type: string description: Full gene name. gene_id: type: integer format: int64 description: Gene ID. hgnc_id: type: - string - 'null' description: Optional HGNC ID. source: type: string description: Source of gene (calculated or submitted). relationship_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGeneVariantRelationship' description: Relationship between gene and variant. ClinvarAlleleName: type: object description: Local type for allele name. required: - value properties: value: type: string description: The name's value. type: type: - string - 'null' description: The name's type. ClinvarAlleleScv: type: object description: |- This is a record per variant (Measure/@ID,AlleleID) as submitted for accessioning in an SCV. Corresponds to "typeAlleleSCV" in XSD. required: - genes - other_names - protein_changes - xrefs - citations - comments - molecular_consequences - functional_consequences - attributes properties: genes: type: array items: $ref: '#/components/schemas/ClinvarAlleleScvGene' description: |- 0 to many genes (and related data ) related to the allele being reported. name: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarOtherName' description: Name provided by the submitter. variant_type: type: - string - 'null' description: Variant type. location: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarLocation' description: Location. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: List of other names. protein_changes: type: array items: type: string description: |- Single letter representation of the amino acid change and its location. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. molecular_consequences: type: array items: $ref: '#/components/schemas/ClinvarMolecularConsequence' description: |- Currently redundant with the MolecularConsequence element of the HGVS element? functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: Functional consequences. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: Attributes. allele_id: type: - integer - 'null' format: int64 description: Allele ID. ClinvarAlleleScvGene: type: object description: |- Local type for Gene. nested elements required: - properties - xrefs properties: name: type: - string - 'null' description: Gene name. properties: type: array items: type: string description: |- Used to set key words for retrieval or display about a gene, such as genes listed by the ACMG guidelines. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: |- Used for gene specific identifiers such as MIM number, Gene ID, HGNC ID, etc. symbol: type: - string - 'null' description: Optional gene symbol. relationship_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGeneVariantRelationship' description: Relationship between gene and variant. ClinvarAssemblyStatus: type: string description: Local enum for the assembly status. enum: - current - previous ClinvarAssertion: type: string description: Enumeration describing assertion type attributes. enum: - variation_to_disease - variation_to_included_disease - variation_in_modifier_gene_to_disease - confers_sensitivity - confers_resistance - variant_to_named_protein ClinvarAttribute: type: object description: Extend the BaseAttribute with a `type` field. required: - type properties: base: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarBaseAttribute' description: The base value. type: type: string description: The type of the attribute. ClinvarAttributeSetElement: type: object description: |- Common type for an entry in a set of attributes. Called ``typeAttributeSet`` in XSD. required: - xrefs - citations - comments properties: attribute: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAttribute' description: The attribute value. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. ClinvarAttributeSetElementType: type: string description: Local enum for types. enum: - mode_of_inheritance - penetrance - age_of_onset - severity - classification_history - severity_description - assertion_method ClinvarBaseAttribute: type: object description: |- The attribute is a general element to represent a defined set of data qualified by an enumerated set of types. For each attribute element, the value will be a character string and is optional. Source shall be used to store identifiers for supplied data from source other than the submitter (e.g. SequenceOntology). The data submitted where Type="variation" shall be validated against sequence_alternation in Sequence Ontology This is to be a generic version of AttributeType and should be used with extension when it is used to specify Type and its enumerations. properties: value: type: - string - 'null' description: The attribute's value; can be empty. integer_value: type: - integer - 'null' format: int64 description: The optional integer value. date_value: type: - string - 'null' format: date-time description: The optional date value. ClinvarChromosome: type: string description: Enumeration describing chromosome. enum: - chromosome1 - chromosome2 - chromosome3 - chromosome4 - chromosome5 - chromosome6 - chromosome7 - chromosome8 - chromosome9 - chromosome10 - chromosome11 - chromosome12 - chromosome13 - chromosome14 - chromosome15 - chromosome16 - chromosome17 - chromosome18 - chromosome19 - chromosome20 - chromosome21 - chromosome22 - x - y - mt - par - un ClinvarCitation: type: object description: Description of a citation. required: - ids properties: ids: type: array items: $ref: '#/components/schemas/ClinvarIdType' description: Optional list of IDs. url: type: - string - 'null' description: Optional URL. citation_text: type: - string - 'null' description: Optional citation text. type: type: - string - 'null' description: |- This maintained distinct from publication types in PubMed and established by GTR curators. The default is 'general'. abbrev: type: - string - 'null' description: Corresponds to the abbreviation reported by GTR. ClinvarClassificationScore: type: object description: Classification score description. required: - value properties: value: type: number format: double description: The score's value. type: type: - string - 'null' description: The score's type; optional. ClinvarClassificationScv: type: object description: |- Report classification of a variant for a SCV. Corresponds to `ClassificationTypeSCV` in XSD. required: - review_status - classification_scores - xrefs - citations - comments properties: review_status: $ref: '#/components/schemas/ClinvarSubmitterReviewStatus' description: The field's review status. germline_classification: type: - string - 'null' description: |- The germline classification; mutually exlusive with `somatic_clinical_impact` and `oncogenicity_classification`. somatic_clinical_impact: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarClassificationScvSomaticClinicalImpact' description: |- Information on the clinical impact; mutually exlusive with `germline_classification` and `oncogenicity_classification`. oncogenicity_classification: type: - string - 'null' description: |- The oncogenicity classification; mutually exlusive with `germline_classification` and `oncogenicity_classification`. explanation_of_classification: type: - string - 'null' description: Optional explanation of classification. classification_scores: type: array items: $ref: '#/components/schemas/ClinvarClassificationScore' description: List of classification scores. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. date_last_evaluated: type: - string - 'null' format: date-time description: Date of last evaluation. ClinvarClassificationScvSomaticClinicalImpact: type: object description: Clinical impact of a somatic variatn. required: - value properties: value: type: string description: The somatic clinical impact value. clinical_impact_assertion_type: type: - string - 'null' description: Type of the clinical impact assertion. clinical_impact_clinical_significance: type: - string - 'null' description: Clinical impact significance. drug_for_therapeutic_assertion: type: - string - 'null' description: Name of the drug for the therapeutic assertion. ClinvarClassifiedCondition: type: object description: |- Interpreted condition for an RCV record. Corresponds to `typeRCVInterpretedCondition` in XSD. required: - value properties: value: type: string description: Condition value. db: type: - string - 'null' description: Database name. id: type: - string - 'null' description: Identifier in database. ClinvarClassifiedRecord: type: object description: |- This element is restricted to variation records for which an explicit classification was submitted. Compare to IncludedRecord, which provides aggregate information about variants that are part of another submission, but for which ClinVar has *not* received a submission specific to that variant independently. required: - clinical_assertions - trait_mappings - deleted_scvs - general_citations properties: simple_allele: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAllele' description: |- Describes a single sequence change relative to a contiguous region of a chromosome or the mitochondrion. Mutually exclusive with `haplotype` and `genotype`. haplotype: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarHaplotype' description: |- Describes multiple sequence changes on one of the chromosomes of a homologous pair or on the mitochondrion. Mutually exclusive with `simple_allele` and `genotype`. genotype: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGenotype' description: |- Describes the combination of sequence changes on each chromosome of a homologous pair. Mutually exclusive with `simple_allele` and `haplotype`. rcv_list: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvList' description: List of RCV records. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: List of classifications. clinical_assertions: type: array items: $ref: '#/components/schemas/ClinvarClinicalAssertion' description: List of clinical assertions. trait_mappings: type: array items: $ref: '#/components/schemas/ClinvarRcvTraitMapping' description: |- This element is used to report how each user-submitted trait name was mapped to a MedGen CUI identifier and a preferred name. The structure may be used in the future to report, when a trait is identified by a source's identifier (e.g. MIM number), the preferred name used by that source at the time of submission. For MappingType XRef, MappingRef is the database name and MappingValue is the database's identifier. For MappingType Name, MappingRef is Alternate or Preferred, and MappingValue is the submitted name of the trait. ClinicalAssertionID is an integer identifier that corresponds 1:1 to the SCV assigned to the submission. deleted_scvs: type: array items: $ref: '#/components/schemas/ClinvarDeletedScv' description: List of deleted SCVs. general_citations: type: array items: $ref: '#/components/schemas/ClinvarGeneralCitations' description: List of general citations. ClinvarClassifiedVariation: type: object description: Local type for tag `ClassifiedVariation`. required: - variation_id - version properties: variation_id: type: integer format: int64 description: Variation ID. accession: type: - string - 'null' description: Optional accession. version: type: integer format: int32 description: Version. ClinvarClinicalAssertion: type: object description: |- A clinical assertion as submitted (SCV record). Corresponds to `MeasureTraitType` in XSD and `` in XML required: - additional_submitters - record_status - replaces - replaceds - assertion - attributes - observed_ins - citations - comments - submission_names properties: clinvar_submission_id: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSubmissionId' description: The ClinVar submission ID. clinvar_accession: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAccession' description: The ClinVar SCV accessions. additional_submitters: type: array items: $ref: '#/components/schemas/ClinvarSubmitter' description: Optional list of additional submitters. record_status: $ref: '#/components/schemas/ClinvarClinicalAssertionRecordStatus' description: Record status. replaces: type: array items: type: string description: Replaces; mutually exclusive with replaceds replaceds: type: array items: $ref: '#/components/schemas/ClinvarClinicalAssertionRecordHistory' description: Replaced list; mutually exclusive with replaces classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarClassificationScv' description: SCV classification. assertion: $ref: '#/components/schemas/ClinvarAssertion' description: The assertion. attributes: type: array items: $ref: '#/components/schemas/ClinvarClinicalAssertionAttributeSetElement' description: Attributes. observed_ins: type: array items: $ref: '#/components/schemas/ClinvarObservedIn' description: Observed in. simple_allele: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAlleleScv' description: Allele in SCV; mutually exclusive with haplotype/genotype. haplotype: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarHaplotypeScv' description: Haplotype in SCV; mutually exclusive with allele/genotype. genotype: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGenotypeScv' description: Genotype in SCV; mutually exclusive with allele/haplotype. trait_set: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarTraitSet' description: The trait set. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. study_name: type: - string - 'null' description: Optional study name. study_description: type: - string - 'null' description: Optional study description. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. submission_names: type: array items: type: string description: List of submissions. date_created: type: - string - 'null' format: date-time description: Date of creation. date_last_updated: type: - string - 'null' format: date-time description: Date of creation. submission_date: type: - string - 'null' format: date-time description: Date of creation. id: type: - integer - 'null' format: int64 description: ID. minimum: 0 fda_recognized_database: type: - boolean - 'null' description: Whether it is an FDA recognized database. ClinvarClinicalAssertionAttributeSetElement: type: object description: Local type for attribute set. required: - type - xrefs - citations - comments properties: attribute: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarBaseAttribute' description: The base value. type: $ref: '#/components/schemas/ClinvarAttributeSetElementType' description: The type of the attribute. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. ClinvarClinicalAssertionRecordHistory: type: object description: |- Inside ClinicalAssertion, a structure to support reporting of an accession, its version, the date its status changed, and text describing that change. Corresponds to `typeClinicalAssertionRecordHistory` in XSD. required: - accession properties: comment: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: Optional comment. accession: type: string description: Accession. version: type: - integer - 'null' format: int32 description: Optional version. date_changed: type: - string - 'null' format: date-time description: Date of the record. ClinvarClinicalAssertionRecordStatus: type: string description: Local enum for record status. enum: - current - replaced - removed ClinvarClinicalFeaturesAffectedStatusType: type: string description: Enumeration describing clinical features affected status. enum: - present - absent - not_tested ClinvarClinicalSignificance: type: object description: |- Describes the clinical significance of a variant. Corresponds to `ClinicalSignificanceType` in XSD. contained elements required: - xrefs - citations - comments properties: review_status: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSubmitterReviewStatus' description: The optional review status. description: type: - string - 'null' description: |- Structure used to support old data of AlleleDescriptionSet within Co-occurenceSet. NB: unused in XML explanation: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: |- Optional explanatory comment. Explanation is used only when the description is 'conflicting data from submitters' The element summarizes the conflict. NB: unused in XML xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Optional list of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Optional list of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Optional list of comments. date_last_evaluated: type: - string - 'null' format: date-time description: |- Date of last evaluation. NB: unused in XML ClinvarComment: type: object description: |- A structure to support reporting unformatted content, with type and source specified. required: - value properties: value: type: string description: The comment's value. data_source: type: - string - 'null' description: The optional comment data source. type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarCommentType' description: The comment's type. ClinvarCommentType: type: string description: Enumeration describing comment type. enum: - public - converted_by_ncb - missing_from_assembly - genomic_location_not_established - location_on_genome_and_product_not_aligned - deletion_comment - merge_comment - assembly_specific_allele_definition - alignment_gap_makes_appear_inconsistent - explanation_of_classification - flagged_comment ClinvarCooccurrence: type: object description: This refers to the zygosity of the variant being asserted. required: - allele_descriptions properties: zygosity: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarZygosity' description: Optional zygosity. allele_descriptions: type: array items: $ref: '#/components/schemas/ClinvarAlleleDescription' description: The allele descriptions. count: type: - integer - 'null' format: int32 description: The optional count. ClinvarDeletedScv: type: object description: |- A structure to support reporting of an accession, its version, the date it was deleted and a free-text summary of why it was deleted. Corresponds to `typeDeletedSCV`. required: - accession - version properties: accession: type: string description: The accession. version: type: integer format: int32 description: The version. date_deleted: type: - string - 'null' format: date-time description: The date of deletion. ClinvarDescriptionHistory: type: object description: |- Description of the history of a record. Called ``typeDescriptionHistory`` in XSD. required: - description properties: description: type: string description: The pathogenicity description. dated: type: - string - 'null' format: date-time description: The date of the description. ClinvarDosageSensitivity: type: object description: |- Haploinsufficiency/Triplosensitivity of gene. nested elements required: - value properties: value: type: string description: Value. last_evaluated: type: - string - 'null' format: date-time description: Optional last evaluated date. clingen: type: - string - 'null' description: URL to ClinGen. ClinvarEvidenceType: type: string description: |- Enumeration describing evidence type. Corresponds to "EvidenceType" in XSD. enum: - genetic - experimental - population - computational ClinvarExtractedRcvRecord: type: object description: Protocol buffer for storing essential information of one RCV. required: - title properties: accession: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarVersionedAccession' description: The accession. title: type: string description: Title of RCV. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvClassifications' description: Classifications (thinned out). ClinvarExtractedVariationType: type: string description: Enumeration for the type of the variant. enum: - insertion - deletion - snv - indel - duplication - tandem_duplication - structural_variant - copy_number_gain - copy_number_loss - protein_only - microsatellite - inversion - other ClinvarExtractedVcvRecord: type: object description: Protocol buffer for storing essential information of one VCV. required: - rcvs - name - variation_type - clinical_assertions - hgnc_ids properties: accession: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarVersionedAccession' description: The accession. rcvs: type: array items: $ref: '#/components/schemas/ClinvarExtractedRcvRecord' description: List of aggregated RCVs. name: type: string description: Name of VCV. variation_type: $ref: '#/components/schemas/ClinvarExtractedVariationType' description: The type of the variant. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Classifications (thinned out). clinical_assertions: type: array items: $ref: '#/components/schemas/ClinvarClinicalAssertion' description: Clinical assertions (thinned out), sequence_location: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSequenceLocation' description: The sequence location on one reference. hgnc_ids: type: array items: type: string description: List of HGNC IDs. ClinvarFamilyData: type: object description: |- Structure to describe attributes of any family data in an observation. If the details of the number of families and the de-identified pedigree id are not available, use FamilyHistory to describe what type of family data is available. Can also be used to report 'Yes' or 'No' if there are no more details. Corresponds to "FamilyInfo" in XSD. nested elements properties: family_history: type: - string - 'null' description: Optional family history. num_families: type: - integer - 'null' format: int32 description: Number of families. num_families_with_variant: type: - integer - 'null' format: int32 description: Number of families with variant. num_families_with_segregation_observed: type: - integer - 'null' format: int32 description: Number of families with segregation observed. pedigree_id: type: - string - 'null' description: Pedigree ID. segregation_observed: type: - string - 'null' description: Segregation oberved (yes, no, number) ClinvarFunctionalConsequence: type: object description: |- Description of a functional consequence. Corresponds to `typeFunctionalConsequence` in XSD. nested elements required: - xrefs - citations - comments - value properties: xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. value: type: string description: Value of functional consequence. ClinvarGender: type: string description: Local enumeration for gender. enum: - male - female - mixed ClinvarGeneVariantRelationship: type: string description: |- Enumeration describing connection between genes and variants. Corresponds to XSD type "GeneVariantRelationship". enum: - variant_within_gene - gene_overlapped_by_variant - near_gene_upstream - near_gene_downstream - asserted_but_not_computed - within_multiple_genes_by_overlap - within_single_gene ClinvarGeneralCitations: type: object description: Type for the tag `GeneralCitations`. required: - xrefs - citations properties: xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. ClinvarGenericSetElement: type: object description: |- Entry in an element set. Called ``SetElementSetType`` in XSD. required: - value - type - citations - xrefs - comments properties: value: type: string description: The element's value. type: type: string description: The element's type. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. ClinvarGenotype: type: object description: |- Used to report genotypes, be they simple or complex diplotypes. Corresponds to "typeGenotype" in XSD. nested elements required: - simple_alleles - haplotypes - name - variation_type - other_names - hgvs_expressions - functional_consequences - xrefs - citations - comments - attributes properties: simple_alleles: type: array items: $ref: '#/components/schemas/ClinvarAllele' description: Simple allele; mutually exclusive with `haplotype`. haplotypes: type: array items: $ref: '#/components/schemas/ClinvarHaplotype' description: |- Haplotype; mutually exclusive with `simple_allele`. Allows more than 2 haplotypes per genotype to support representation of ploidy. name: type: string description: Optional name. variation_type: $ref: '#/components/schemas/ClinvarVariationType' description: The variation type. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: Names other than 'preferred' used for the Genotype. hgvs_expressions: type: array items: $ref: '#/components/schemas/ClinvarHgvsExpression' description: HGVS descriptions. functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: Functional consequences. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Aggregated classifications. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: Attributes. variation_id: type: - integer - 'null' format: int64 description: Variation ID. ClinvarGenotypeScv: type: object description: |- Used to report genotypes, be they simple or complex diplotypes. Corresponds to "typeGenotypeSCV" in XSD. nested elements required: - simple_alleles - haplotypes - other_names - variation_type - functional_consequences - attributes - citations - xrefs - comments properties: simple_alleles: type: array items: $ref: '#/components/schemas/ClinvarAlleleScv' description: Simple alleles; mutually exclusive with `haplotypes`. haplotypes: type: array items: $ref: '#/components/schemas/ClinvarHaplotypeScv' description: |- Haplotype; mutually exclusive with `simple_alleles`. Allows more than 2 haplotypes per genotype to support representation of ploidy. name: type: - string - 'null' description: Optional name. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: Other names used for the genotype. variation_type: $ref: '#/components/schemas/ClinvarVariationType' description: The variation type. functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: Functional consequences. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: Attributes. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. variation_id: type: - integer - 'null' format: int64 description: Variation ID. ClinvarGlobalMinorAlleleFrequency: type: object description: Local type for GlobalMinorAlleleFrequency. required: - value - source properties: value: type: number format: double description: Value. source: type: string description: Source. minor_allele: type: - string - 'null' description: Minor allele. url: type: - string - 'null' description: URL. ClinvarHaploVariationType: type: string description: Enumeration describing haplotype variation types. enum: - haplotype - haplotype_single_variant - variation - phase_unknown - haplotype_defined_by_single_variant ClinvarHaplotype: type: object description: |- This is a record of one or more simple alleles on the same chromosome molecule. Corresponds to `typeHaplotype` in XSD required: - simple_alleles - name - variation_type - other_names - hgvs_expressions - functional_consequences - xrefs - comments - variation_id properties: simple_alleles: type: array items: $ref: '#/components/schemas/ClinvarAllele' description: The list of alleles in the haplotype. name: type: string description: The preferred representation of the haplotype. variation_type: $ref: '#/components/schemas/ClinvarVariationType' description: The type of the haplotype. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: Names other than 'preferred' used for the haplotype. hgvs_expressions: type: array items: $ref: '#/components/schemas/ClinvarHgvsExpression' description: |- List of all the HGVS expressions valid for, or used to submit, a variant. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Classifications of the variant. functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: Functional consequences of the variant. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of cross-references. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. variation_id: type: integer format: int64 description: Variation ID. number_of_copies: type: - integer - 'null' format: int32 description: Number of copies. number_of_chromosomes: type: - integer - 'null' format: int32 description: Number of chromosomes. ClinvarHaplotypeScv: type: object description: |- This is a record of a haplotype in SCV. Corresponds to `typeHaplotypeSCV` in XSD. required: - simple_alleles - other_names - functional_consequences - attributes - citations - xrefs - comments properties: simple_alleles: type: array items: $ref: '#/components/schemas/ClinvarAlleleScv' description: The list of alleles in the haplotype. name: type: - string - 'null' description: The preferred representation of the haplotype. other_names: type: array items: $ref: '#/components/schemas/ClinvarOtherName' description: Names other than 'preferred' used for the haplotype. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Classification of the variant. functional_consequences: type: array items: $ref: '#/components/schemas/ClinvarFunctionalConsequence' description: Functional consequences of the variant. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: List of attributes. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of cross-references. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. variation_id: type: - integer - 'null' format: int64 description: Variation ID. number_of_copies: type: - integer - 'null' format: int32 description: Number of copies. number_of_chromosomes: type: - integer - 'null' format: int32 description: Number of chromosomes. ClinvarHgvsExpression: type: object description: |- A structure to represent an HGVS expression for a nucleotide sequence variant, along with the predicted protein change and the predicted molecular consequence. Also used to represent only the protein change if that is all that has been reported. Corresponds to `typeHVSExpression` in XSD. nested elements required: - molecular_consequences - type properties: nucleotide_expression: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarHgvsNucleotideExpression' description: Optional nucleotide sequence expression. protein_expression: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarHgvsProteinExpression' description: Optional protein sequence expression. molecular_consequences: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of molecular consequences. type: $ref: '#/components/schemas/ClinvarHgvsType' description: Type of HGVS expression. assembly: type: - string - 'null' description: Optional assembly. ClinvarHgvsNucleotideExpression: type: object description: |- Description of a nucleotide sequence expression. Corresponds to `typeNucleotideSequenceExpression` required: - expression properties: expression: type: string description: The expression values. sequence_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarNucleotideSequence' description: The type of the nucleotide sequence. sequence_accession_version: type: - string - 'null' description: Optional sequence accession version. sequence_accession: type: - string - 'null' description: Optional sequence accession. sequence_version: type: - integer - 'null' format: int32 description: Optional sequence version. change: type: - string - 'null' description: Optional description of the change. assembly: type: - string - 'null' description: Optional assembly information. submitted: type: - string - 'null' description: Optional submission information. mane_select: type: - boolean - 'null' description: Optional MANE Select flag. mane_plus_clinical: type: - boolean - 'null' description: Optional MANE Plus Clinical flag. ClinvarHgvsProteinExpression: type: object description: |- Description of a protein sequence expression. Corresponds to `typeProteinSequenceExpression` in XSD. required: - expression properties: expression: type: string description: The expression values. sequence_accession_version: type: - string - 'null' description: Optional sequence accession version. sequence_accession: type: - string - 'null' description: Optional sequence accession. sequence_version: type: - integer - 'null' format: int32 description: Optional sequence version. change: type: - string - 'null' description: Optional description of the change. ClinvarHgvsType: type: string description: Enumeration describing HGVS types. enum: - coding - genomic - genomic_top_level - non_coding - protein ClinvarIdType: type: object description: Local ID with source. required: - value - source properties: value: type: string description: The citation's value. source: type: string description: If there is an identifier, what database provides it. ClinvarIncludedRecord: type: object description: |- This element is used for alleles that were not directly part of a submission but were part of a complex submission. They have no direct submitted classification, but are being reported for a complete representation of all alleles in ClinVar. Compare to ClassifiedRecord. required: - submitted_classifications - classified_variations - general_citations properties: simple_allele: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAllele' description: Simple allele; mutually exclusive with haplotype. haplotype: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarHaplotype' description: Haplotype; mutually exclusive with simple_allele. classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAggregateClassificationSet' description: Aggregate classification sets. submitted_classifications: type: array items: $ref: '#/components/schemas/ClinvarScv' description: List of submitted records. classified_variations: type: array items: $ref: '#/components/schemas/ClinvarClassifiedVariation' description: |- Maintains the list of classified variants represented in this submission, although not submitted with an Classification independently. general_citations: type: array items: $ref: '#/components/schemas/ClinvarGeneralCitations' description: List of general citations. ClinvarIndication: type: object description: |- Describes an indication. NB: Called "IndicationType" in the XSD. required: - traits - names - attributes - xrefs - citations - comments - type properties: traits: type: array items: $ref: '#/components/schemas/ClinvarTrait' description: Represents the value for the test indication as a name of a trait. names: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: List of names. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: List of attributes. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. type: $ref: '#/components/schemas/ClinvarIndicationType' description: The type of indication. ClinvarIndicationType: type: string description: Enumeration for the indication type. enum: - indication ClinvarLocation: type: object description: |- There can be multiple types of location, and the locations may have identifiers in other databases. Corresponds to `typeLocation` in XSD. required: - cytogenetic_locations - sequence_locations - gene_locations - xrefs properties: cytogenetic_locations: type: array items: type: string description: |- Cytogenetic location is maintained independent of sequence location, and can be submitted or computed from the sequence location. Between 0 and 4 entries. sequence_locations: type: array items: $ref: '#/components/schemas/ClinvarSequenceLocation' description: |- Location on a defined sequence, with reference and alternate allele, and start /stop values depending on the specificity with which the variant location is known. The number system of offset 1, and right-justified to be consistent with HGVS location data. gene_locations: type: array items: type: string description: The location of the variant relative to features within the gene. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. ClinvarMethod: type: object description: |- Details of a method used to generate variant calls or predict/report functional consequence. The name of the platform should represent a sequencer or an array, e.g. sequencing or array , e.g. capillary, 454, Helicos, Solexa, SOLiD. This structure should also be used if the method is 'Curation'. Corresponds to `MethodType` in XSD. required: - citations - xrefs - software - method_type - method_attributes - obs_method_attributes properties: name_platform: type: - string - 'null' description: Platform name. type_platform: type: - string - 'null' description: Platform type. purpose: type: - string - 'null' description: Method purpose. result_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarResultType' description: Method result type. min_reported: type: - string - 'null' description: Smallest reported. max_reported: type: - string - 'null' description: Largest reported. reference_standard: type: - string - 'null' description: Reference standard. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. description: type: - string - 'null' description: |- Free text to enrich the description of the method and to provide information not captured in specific fields. software: type: array items: $ref: '#/components/schemas/ClinvarSoftware' description: List of softwares used. source_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarMethodSourceType' description: Source type. method_type: $ref: '#/components/schemas/ClinvarMethodListType' description: Method type. method_attributes: type: array items: $ref: '#/components/schemas/ClinvarMethodAttribute' description: Method attribute. obs_method_attributes: type: array items: $ref: '#/components/schemas/ClinvarObsMethodAttribute' description: |- ObsMethodAttribute is used to indicate an attribute specific to a particular method in conjunction with a particular observation . ClinvarMethodAttribute: type: object description: Local type for method attribute. required: - type properties: base: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarBaseAttribute' description: The base value. type: $ref: '#/components/schemas/ClinvarMethodAttributeType' description: The attribute type. ClinvarMethodAttributeType: type: string description: Local enumeration of attribute type. enum: - location - controls_appropriate - method_appropriate - test_name - struct_var_method_type - probe_accession ClinvarMethodListType: type: string description: |- Enumeration describing method list. Corresponds to "MethodListType" in XSD. enum: - literature_only - reference_population - case_control - clinical_testing - in_vitro - in_vivo - research - curation - not_provided - provider_interpretation - phenotyping_only ClinvarMethodSourceType: type: string description: Local enumeration for SourceType. enum: - submitter_generated - data_mining - data_review ClinvarMethodType: type: string description: Local enum for the method type. enum: - literature_only - reference_population - case_control - clinical_testing - in_vitro - in_vivo - inferred_from_source - research ClinvarMolecularConsequence: type: object description: |- Local type for MolecularConsequence. nested elements required: - xrefs - citations - comments - function properties: xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Xref list. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Citation list. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Comment list. rs: type: - integer - 'null' format: int64 description: RS id. hgvs: type: - string - 'null' description: Optional HGVS expression. so_id: type: - string - 'null' description: Optional SO id. function: type: string description: Function. ClinvarNucleotideSequence: type: string description: Enumeration describing nucleotide sequence. enum: - genomic_top_level - genomic_ref_seq_gene - genomic - coding - non_coding - protein ClinvarObsMethodAttribute: type: object description: Local type for observation method attribute. required: - type - comments properties: base: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarBaseAttribute' description: The base value. type: $ref: '#/components/schemas/ClinvarObsMethodAttributeType' description: The attribute type. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Optional comments. ClinvarObsMethodAttributeType: type: string description: Local enumeration for attribute type. enum: - method_result - testing_laboratory ClinvarObservedData: type: object description: |- This is an AttributeSet, there will be 1 attribute supported by optional citations, xrefs and comment. There must be at least one ObservedData Set, but can be any number. For each ObservedData set the Attribute will be either decimal or string depending on type. The value will be stored here, but decimals will be entered to the database as a string. required: - attributes - citations - xrefs - comments properties: attributes: type: array items: $ref: '#/components/schemas/ClinvarObservedDataAttribute' description: Attributes. severity: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSeverity' description: Severity. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Citation list. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Xref list. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Comment list. ClinvarObservedDataAttribute: type: object description: Local struct for attributes based on `BaseAttribute`. required: - type properties: base: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarBaseAttribute' description: base type: $ref: '#/components/schemas/ClinvarObservedDataAttributeType' description: type ClinvarObservedDataAttributeType: type: string description: Local enum for the observed data type. enum: - description - variant_alleles - subjects_with_variant - subjects_with_different_causative_variant - variant_chromosomes - independent_observations - single_heterozygous - compound_heterozygous - homozygous - hemizygous - number_mosaic - observed_unspecified - allele_frequency - secondary_finding - genotype_and_moi_consistent - unaffected_family_member_with_causative_variant - het_parent_transmit_normal_allele - cosegregating_families - informative_meioses - sample_local_id - sample_variant_id - family_history - num_families_with_variant - num_families_with_segregation_observed - segregation_observed ClinvarObservedIn: type: object description: |- Documents in what populations or samples an allele or genotype has been observed relative to the described trait. Summary observations can be registered per submitted assertion, grouped by common citation, study type, origin, ethnicity, tissue, cell line, and species data. Not all options are valid per study type, but these will not be validated in the xsd. Corresponds to `ObservationSet` in XSD. required: - observed_data - cooccurrence_sets - citations - xrefs - comments properties: sample: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSample' description: Sample. observed_data: type: array items: $ref: '#/components/schemas/ClinvarObservedData' description: Observed data. cooccurrence_sets: type: array items: $ref: '#/components/schemas/ClinvarCooccurrence' description: Co-occurence set. trait_set: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarTraitSet' description: TraitSet. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Citation list. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Xref list. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Comment list. ClinvarOrigin: type: string description: Enumeration describing origin. enum: - germline - somatic - de_novo - not_provided - inherited - maternal - paternal - uniparental - biparental - not_reported - tested_inconclusive - unknown - not_applicable - experimentally_generated ClinvarOtherName: type: object description: |- A name with an optional type. Corresponds to `typeNames` in XSD. required: - value properties: value: type: string description: The name's value. type: type: - string - 'null' description: The name's type. ClinvarPhenotypeSetType: type: string description: Enumeration describing phenotype set. enum: - disease - drug_response - finding - phenotype_instruction - trait_choice ClinvarProteinSequence: type: string description: Enumeration describing protein sequence. enum: - protein ClinvarRcvAccession: type: object description: Corresponds to "typeRCV" in XSD. required: - replaceds - accession - version properties: classified_condition_list: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvClassifiedConditionList' description: The list of classified conditions. rcv_classifications: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvClassifications' description: The list of RCV classifications. replaceds: type: array items: $ref: '#/components/schemas/ClinvarRecordHistory' description: The list of RCV accessions this record has replaced. title: type: - string - 'null' description: Optional title. accession: type: string description: Accession. version: type: integer format: int32 description: Version. ClinvarRcvAccessionSomaticClinicalImpact: type: object description: |- Local type for SomaticClinicalImpact. The aggregate review status based on all somatic clinical impact submissions for this record. required: - review_status - descriptions properties: review_status: $ref: '#/components/schemas/ClinvarAggregateSomaticClinicalImpactReviewStatus' description: |- The aggregate review status based on all somatic clinical impact submissions for this record. descriptions: type: array items: $ref: '#/components/schemas/ClinvarRcvSomaticClinicalImpactDescription' description: The oncogenicity description. ClinvarRcvClassifications: type: object description: Local type for RCV classifications. properties: germline_classification: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvGermlineClassification' description: Germline classification. somatic_clinical_impact: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvAccessionSomaticClinicalImpact' description: Somatic clinical impact. oncogenicity_classification: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvOncogenicityClassification' description: Oncogenicity classification. ClinvarRcvClassifiedConditionList: type: object description: |- Local type for ClassifiedConditionList. nested elements required: - classified_conditions properties: classified_conditions: type: array items: $ref: '#/components/schemas/ClinvarClassifiedCondition' description: List of interpreted conditions. trait_set_id: type: - integer - 'null' format: int64 description: Trait set ID. ClinvarRcvGermlineClassification: type: object description: |- Local type for GermlineClassification. The aggregate review status based on all germline submissions for this record. required: - review_status properties: review_status: $ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus' description: |- The aggregate review status based on all somatic clinical impact submissions for this record. description: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvGermlineClassificationDescription' description: The oncogenicity description. ClinvarRcvGermlineClassificationDescription: type: object description: Local type for Description. required: - value properties: value: type: string description: The description. date_last_evaluated: type: - string - 'null' format: date-time description: The date of the description. submission_count: type: - integer - 'null' format: int32 description: The number of submissions. minimum: 0 ClinvarRcvList: type: object description: Local type for tag `RCVList`. required: - rcv_accessions properties: rcv_accessions: type: array items: $ref: '#/components/schemas/ClinvarRcvAccession' description: The RCV record. submission_count: type: - integer - 'null' format: int32 description: The number of submissions (SCV accessions) referencing the VariationID. independent_observations: type: - integer - 'null' format: int32 description: The number of idependent observations. ClinvarRcvOncogenicityClassification: type: object description: Local type for OncogenicityClassification. required: - review_status properties: review_status: $ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus' description: |- The aggregate review status based on all oncogenic submissions for this record. description: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRcvOncogenicityDescription' description: The oncogenicity description. ClinvarRcvOncogenicityDescription: type: object description: Local type for Description. required: - value properties: value: type: string description: The description. date_last_evaluated: type: - string - 'null' format: date-time description: The date of the description. submission_count: type: - integer - 'null' format: int32 description: The number of submissions. minimum: 0 ClinvarRcvSomaticClinicalImpactDescription: type: object description: Local type for Description. required: - value properties: value: type: string description: The description. clinical_impact_assertion_type: type: - string - 'null' description: Clinical impact assertion type. clinical_impact_clinical_significance: type: - string - 'null' description: Clinical impact significance date_last_evaluated: type: - string - 'null' format: date-time description: The date of the description. submission_count: type: - integer - 'null' format: int32 description: The number of submissions. minimum: 0 ClinvarRcvTraitMapping: type: object description: Local type for the tag `TraitMapping`. required: - medgens - clinical_assertion_id - trait_type - mapping_type - mapping_value - mapping_ref properties: medgens: type: array items: $ref: '#/components/schemas/ClinvarRcvTraitMappingMedgen' description: nested elements clinical_assertion_id: type: integer format: int64 description: ID of clinical assertion. trait_type: type: string description: The trait type. mapping_type: $ref: '#/components/schemas/ClinvarRcvTraitMappingType' description: The mapping type. mapping_value: type: string description: The mapping value. mapping_ref: type: string description: The mapping reference. ClinvarRcvTraitMappingMedgen: type: object description: Local type for the tag "MedGen" required: - name - cui properties: name: type: string description: Name. cui: type: string description: CUI. ClinvarRcvTraitMappingType: type: string description: Local type for the attribute `@MappingType`. enum: - name - xref ClinvarRecordHistory: type: object description: |- A structure to support reporting of an accession, its version, the date its status changed, and text describing that change. Corresponds to `typeRecordHistory` in XSD. nested elements required: - accession - version properties: comment: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: Optional comment on the history record. accession: type: string description: The accession. version: type: integer format: int32 description: The version. date_changed: type: - string - 'null' format: date-time description: The date the record. variation_id: type: - integer - 'null' format: int64 description: |- Attribute @VaritionID is only populated for VCV, where @Accession is like VCV000000009 ClinvarRelativeOrientation: type: string description: |- Enumeration for relative orientation. NB: unused in XML enum: - cis - trans - unknown ClinvarResultType: type: string description: Local enumeration for result types. enum: - number_of_occurrences - p_value - odds_ratio - variant_call ClinvarSample: type: object description: |- Description of a sample. Corresponds to `typeSample` in XSD. required: - ages - citations - xrefs - comments properties: sample_description: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSampleDescription' description: The sample description. origin: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarOrigin' description: The sample origin. ethnicity: type: - string - 'null' description: Sample ethnicity. geographic_origin: type: - string - 'null' description: Sample geographic origin. tissue: type: - string - 'null' description: Sample tissue. somatic_variant_in_normal_tissue: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSomaticVariantInNormalTissue' description: Presence of variant in normal tissue. somatic_variant_allele_fraction: type: - string - 'null' description: Somatic variant allele fraction. cell_line: type: - string - 'null' description: Cell line name. species: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSpecies' description: Species. ages: type: array items: $ref: '#/components/schemas/ClinvarAge' description: Age (range), max. size of 2. strain: type: - string - 'null' description: Strain. affected_status: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAffectedStatus' description: Affected status. numer_tested: type: - integer - 'null' format: int32 description: Denominator, total individuals included in this observation set. number_males: type: - integer - 'null' format: int32 description: Denominator, total males included in this observation set. number_females: type: - integer - 'null' format: int32 description: Denominator, total females included in this observation set. number_chr_tested: type: - integer - 'null' format: int32 description: |- Denominator, total number chromosomes tested. Number affected and unaffected are captured in the element NumberObserved. gender: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarGender' description: |- Gender should be used ONLY if explicit values are not available for number of males or females, and there is a need to indicate that the genders in the sample are known. family_data: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarFamilyData' description: Family information. proband: type: - string - 'null' description: Optional proband ID. indication: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarIndication' description: Optional indication. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. source_type: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSampleSourceType' description: Source type. ClinvarSampleDescription: type: object description: Local type for sample description. properties: description: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: Description of sample. citation: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarCitation' description: Citation. ClinvarSampleSourceType: type: string description: Local enumeration for SourceType. enum: - submitter_generated - data_mining ClinvarScv: type: object description: |- Description of a SCV. Corresponds to "typeSCV" in XSD. required: - accession - version properties: title: type: - string - 'null' description: Optional title. accession: type: string description: Accession. version: type: integer format: int32 description: Version. ClinvarSequenceLocation: type: object description: Local type for sequence location. required: - assembly - chr properties: for_display: type: - boolean - 'null' description: forDisplay value. assembly: type: string description: Name of assembly. chr: $ref: '#/components/schemas/ClinvarChromosome' description: Chromosomeof variant. accession: type: - string - 'null' description: Optional chromosome accession. outer_start: type: - integer - 'null' format: int32 description: Outer start position. minimum: 0 inner_start: type: - integer - 'null' format: int32 description: Inner start position. minimum: 0 start: type: - integer - 'null' format: int32 description: Start position. minimum: 0 stop: type: - integer - 'null' format: int32 description: Stop position. minimum: 0 inner_stop: type: - integer - 'null' format: int32 description: Inner stop position. minimum: 0 outer_stop: type: - integer - 'null' format: int32 description: Outer stop position. minimum: 0 display_start: type: - integer - 'null' format: int32 description: Display start position. minimum: 0 display_stop: type: - integer - 'null' format: int32 description: Display stop position. minimum: 0 strand: type: - string - 'null' description: Strand. variant_length: type: - integer - 'null' format: int32 description: Variant length. minimum: 0 reference_allele: type: - string - 'null' description: Reference allele. alternate_allele: type: - string - 'null' description: Alternate allele. assembly_accession_version: type: - string - 'null' description: Assembly accession version. assembly_status: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarAssemblyStatus' description: Assembly status. position_vcf: type: - integer - 'null' format: int32 description: Position in VCF. minimum: 0 reference_allele_vcf: type: - string - 'null' description: Reference allele in VCF. alternate_allele_vcf: type: - string - 'null' description: Alternate allele in VCF. for_display_length: type: - integer - 'null' format: int32 description: For display length. minimum: 0 ClinvarSeverity: type: string description: |- Enumeration describing severity. Corresponds to XSD type "typeSeverity" enum: - mild - moderate - severe ClinvarSoftware: type: object description: Description of a software. required: - name properties: name: type: string description: Name of the software. version: type: - string - 'null' description: Version of the software; optional. purpose: type: - string - 'null' description: Purpose of the software; optional. ClinvarSomaticVariantInNormalTissue: type: string description: Local enumeration for presence in normal tissue. enum: - present - absent - not_tested ClinvarSpecies: type: object description: Definition of a species. required: - name properties: name: type: string description: Name of the species. taxonomy_id: type: - integer - 'null' format: int32 description: Optional taxonomy ID. ClinvarStatus: type: string description: |- Enumeration describing status. Corresponds to `typeStatus` in XSD. enum: - current - completed_and_retired - delete - in_development - reclassified - reject - secondary - suppressed - under_review ClinvarSubmissionId: type: object description: Local type for ClinVarSubmissionID. required: - local_key properties: local_key: type: string description: |- The identifier provided by the submitter to facilitate identification of records corresponding to their submissions. If not provided by a submitter, NCBI generates one. If provided by submitter, that is represented in localKeyIsSubmitted. title: type: - string - 'null' description: Optional title. local_key_is_submitted: type: - boolean - 'null' description: Optional indication whether local key has been submitted. submitted_assembly: type: - string - 'null' description: Optional assembly of submission. ClinvarSubmitter: type: object description: |- A structure to support reporting the name of a submitter, its organization id, and its abbreviation and type. required: - type properties: submitter_identifiers: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSubmitterIdentifiers' description: The submitter's identifier. type: $ref: '#/components/schemas/ClinvarSubmitterType' description: The submitter type. ClinvarSubmitterIdentifiers: type: object description: |- Set of attributes for the primary submitter. Any addtional submitters are captured in the AdditionalSubmitters element. required: - submitter_name - org_id - org_category properties: submitter_name: type: string description: Name of submitter. org_id: type: integer format: int64 description: Organization ID. org_category: type: string description: Organization category. org_abbreviation: type: - string - 'null' description: Organization abbreviation; optional. ClinvarSubmitterReviewStatus: type: string description: |- Enumeration describing submitter review status. Corresponds to `typeSubmitterReviewStatusValue` in XSD. enum: - no_classification_provided - no_assertion_criteria_provided - criteria_provided_single_submitter - reviewed_by_expert_panel - practice_guideline - flagged_submission - criteria_provided_multiple_submitters_no_conflicts - criteria_provided_conflicting_classifications - classified_by_single_submitter - reviewed_by_professional_society - not_classified_by_submitter - classified_by_multiple_submitters ClinvarSubmitterType: type: string description: Enumeration of submitter kind. enum: - primary - secondary - behalf ClinvarTrait: type: object description: Type to describe traits in various places. required: - names - symbols - attributes - trait_relationships - citations - xrefs - comments - sources properties: names: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: names symbols: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: symbols attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: attributes trait_relationships: type: array items: $ref: '#/components/schemas/ClinvarTraitRelationship' description: Trait relationships citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Citation list. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Xref list. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Comment list. sources: type: array items: type: string description: Sources ClinvarTraitRelationship: type: object description: Local type for trait relationship. required: - names - citations - xrefs - comments - sources - type properties: names: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: Name(s) of the trait. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: Citation list. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: Xref list. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: Comment list. sources: type: array items: type: string description: Sources type: $ref: '#/components/schemas/ClinvarTraitRelationshipType' description: Trait type. ClinvarTraitRelationshipType: type: string description: |- Local enumeration for trait types. NB: only DrugResponseAndDisease is used in the XML. enum: - phenotype - subphenotype - drug_response_and_disease - co_occuring_condition - finding_member ClinvarTraitSet: type: object description: |- A set of ``Trait`` objects. NB: Called "ClinAsserTraitSetType" in the XSD. required: - traits - names - symbols - attributes - xrefs - citations - comments - type properties: traits: type: array items: $ref: '#/components/schemas/ClinvarTrait' description: The traits. names: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: The names. symbols: type: array items: $ref: '#/components/schemas/ClinvarGenericSetElement' description: The symbols. attributes: type: array items: $ref: '#/components/schemas/ClinvarAttributeSetElement' description: The attributes. xrefs: type: array items: $ref: '#/components/schemas/ClinvarXref' description: List of xrefs. citations: type: array items: $ref: '#/components/schemas/ClinvarCitation' description: List of citations. comments: type: array items: $ref: '#/components/schemas/ClinvarComment' description: List of comments. type: $ref: '#/components/schemas/ClinvarTraitSetType' description: The type. date_last_evaluated: type: - string - 'null' format: date-time description: Date of last evaluation. id: type: - integer - 'null' format: int64 description: ID. contributes_to_aggregate_classification: type: - boolean - 'null' description: Whether contributes to aggregate classification. lower_level_of_evidence: type: - boolean - 'null' description: Lower level of evidence. multiple_condition_explanation: type: - string - 'null' description: Explanation of or multiple conditions. ClinvarTraitSetType: type: string description: Local type. enum: - disease - drug_response - finding - phenotype_instruction - trait_choice ClinvarVariationArchive: type: object description: |- This element groups the set of data specific to a VariationArchive record, namely the summary data of what has been submitted about a VariationID AND for Classified records only, the content each submission (SCV) provided. Type for the `` type. required: - variation_id - variation_name - variation_type - accession - version - number_of_submitters - number_of_submissions - record_type - record_status - replaceds properties: variation_id: type: integer format: int64 description: Numeric variation ID. variation_name: type: string description: |- This is ClinVar's name for the variant. ClinVar uses this term in its web displays variation_type: type: string description: Type of the variant. date_created: type: - string - 'null' format: date-time description: |- DateCreated is the date when the record first became public in ClinVar. date_last_updated: type: - string - 'null' format: date-time description: |- The date the record was last updated in the public database. The update may be a change to one of the submitted records (SCVs) or annotation added to the aggregate record by NCBI staff. This date is independent of a version change; annotated added by NCBI may change without representing a change in the version. most_recent_submission: type: - string - 'null' format: date-time description: |- This date is of the most recent submitted record (SCV) for the VCV; it may reflect a new submitted record or an update to a submitted record. accession: type: string description: |- Accession assigned to the variant, or set of variants, that was Classified version: type: integer format: int32 description: Version of record and suffix for accession. number_of_submitters: type: integer format: int32 description: Number of submitters in record. number_of_submissions: type: integer format: int32 description: Number of submissions in record. record_type: $ref: '#/components/schemas/ClinvarVariationArchiveRecordType' description: Record type. record_status: $ref: '#/components/schemas/ClinvarVariationArchiveRecordStatus' description: The record's status. replaced_by: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarRecordHistory' description: Pointer to the replacing record; optional. replaceds: type: array items: $ref: '#/components/schemas/ClinvarRecordHistory' description: The list of VCV accessions this record has replaced. comment: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarComment' description: Comment on the record; optional. species: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarSpecies' description: Specification of the species. classified_record: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarClassifiedRecord' description: |- This element describes the classification of a single allele, haplotype, or genotype based on all submissions to ClinVar. This differs from the element IncludedRecord, which describes simple alleles or haplotypes, referenced in ClassifiedRecord, but for which no explicit classification was submitted. Once that variation is described, details are added about the phenotypes being classified, the classification, the submitters providing the classifications, and all supported evidence. NB: mutually exclusive with `included_record`. included_record: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarIncludedRecord' description: |- This element describes a single allele or haplotype included in submissions to ClinVar, but for which no explicit classification was submitted. It also references the submissions and the Classified records that include them. NB: mutually exclusive with `classified_record`. ClinvarVariationArchiveRecordStatus: type: string description: Enumeration for `@RecordStatus`. enum: - current - previous - replaced - deleted ClinvarVariationArchiveRecordType: type: string description: Enumeration for `@RecordType`. enum: - included - classified ClinvarVariationRelease: type: object description: |- The element to group each VariationArchive element in the release Type for the `` tag. attributes required: - variation_archives properties: release_date: type: - string - 'null' format: date-time description: The current release. variation_archives: type: array items: $ref: '#/components/schemas/ClinvarVariationArchive' description: List of `` tags. ClinvarVariationType: type: string description: Enumeration describing variation type. enum: - diplotype - compound_heterozygote - distinct_chromosomes ClinvarVersionedAccession: type: object description: Accession with version. required: - accession - version properties: accession: type: string description: The accession. version: type: integer format: int32 description: The version. ClinvarXref: type: object description: |- This structure is used to represent how an object described in the submission relates to objects in other databases. required: - db - id properties: db: type: string description: |- The name of the database. When there is an overlap with sequence databases, that name is used. id: type: string description: |- The identifier used by the database. Being exported as a string even though internally the database has rules for defining which datases use integer identifers. type: type: - string - 'null' description: |- Used to differentiate between different types of identifiers that a database may provide. url: type: - string - 'null' description: Optional URL to the database entry. status: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarStatus' description: The status; defaults to "current". ClinvarZygosity: type: string description: Enumeration describing zygosity. enum: - homozygote - single_heterozygote - compound_heterozygote - hemizygote - not_provided CustomError: type: object description: Custom error type for the Actix server. required: - err properties: err: type: string DbsnpRecord: type: object description: A record corresponding to dbSNP VCF. required: - chrom - pos - ref_allele - alt_allele - rs_id properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: Alternate allele. rs_id: type: integer format: int32 description: The rs ID. ExtractedVcvRecordList: type: object description: List of `ClinvarExtractedVcvRecord`s. required: - records properties: records: type: array items: $ref: '#/components/schemas/ClinvarExtractedVcvRecord' description: The list of VCV records that may share a global variant. GeneNames: type: object description: Identifier / name information for one gene. required: - hgnc_id - symbol - name - alias_symbol - alias_name properties: hgnc_id: type: string description: HGNC gene ID. symbol: type: string description: HGNC gene symbol. name: type: string description: Gene name from HGNC. alias_symbol: type: array items: type: string description: HGNC alias symbols. alias_name: type: array items: type: string description: HGNC alias names. ensembl_gene_id: type: - string - 'null' description: ENSEMBL gene ID. ncbi_gene_id: type: - string - 'null' description: NCBI gene ID. GenesAcmgSecondaryFindingRecord: type: object description: Information from ACMG secondary findings list. required: - hgnc_id - ensembl_gene_id - ncbi_gene_id - gene_symbol - mim_gene_id - disease_phenotype - disorder_mim - phenotype_category - inheritance - sf_list_version - variants_to_report properties: hgnc_id: type: string description: The HGNC ID. ensembl_gene_id: type: string description: The Ensembl gene ID. ncbi_gene_id: type: string description: The NCBI gene ID. gene_symbol: type: string description: The HGNC gene symbol. mim_gene_id: type: string description: The MIM gene ID. disease_phenotype: type: string description: The disease phenotype. disorder_mim: type: string description: The disease MIM id. phenotype_category: type: string description: The phenotype category. inheritance: type: string description: The mode of inheritance. sf_list_version: type: string description: The version of the ACMG SF list of first appearance. variants_to_report: type: string description: The variants to report according to ACMG SF. GenesClingenDosageRecord: type: object description: '`ClinGen` gene dosage sensitivity record.' required: - gene_symbol - ncbi_gene_id - genomic_location_37 - genomic_location_38 properties: gene_symbol: type: string description: Gene symbol. ncbi_gene_id: type: string description: NCBI gene ID. genomic_location_37: type: string description: Genomic location GRCh37. genomic_location_38: type: string description: Genomic location GRCh38. haploinsufficiency_score: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesClingenDosageScore' description: Haploinsufficiency score. triplosensitivity_score: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesClingenDosageScore' description: Triplosensitivity score. haploinsufficiency_disease_id: type: - string - 'null' description: Haploinsufficiency Disease ID. triplosensitivity_disease_id: type: - string - 'null' description: Haploinsufficiency Disease ID. GenesClingenDosageScore: type: string description: Enumeration for Haploinsufficiency / Triplosensitivity scores. enum: - SufficientEvidenceAvailable - SomeEvidenceAvailable - LittleEvidence - NoEvidenceAvailable - Recessive - Unlikely GenesClinvarPerGeneRecord: type: object description: ClinVar detailed information per gene. required: - per_release_vars properties: per_impact_counts: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGeneImpactCounts' description: Counts of variants per impact per_freq_counts: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesCoarseClinsigFrequencyCounts' description: Counts of variants per impact / frequency per_release_vars: type: array items: $ref: '#/components/schemas/GenesExtractedVariantsPerRelease' description: Variants for the given gene. GenesClinvarQuery: type: object description: Parameters for `handle`. properties: hgnc_id: type: - array - 'null' items: type: string description: The HGNC IDs to search for. GenesClinvarResponse: type: object description: Result for `handle_with_openapi`. required: - genes properties: genes: type: array items: $ref: '#/components/schemas/GenesClinvarResponseEntry' description: The resulting per-gene ClinVar information. GenesClinvarResponseEntry: type: object description: One entry in the result. required: - hgnc_id - record properties: hgnc_id: type: string description: HGNC ID of the gene. record: $ref: '#/components/schemas/GenesClinvarPerGeneRecord' description: The resulting per-gene record. GenesCoarseClinsigFrequencyCounts: type: object required: - hgnc_id - pathogenic_counts - uncertain_counts - benign_counts properties: hgnc_id: type: string description: The gene HGNC ID. pathogenic_counts: type: array items: type: integer format: int32 minimum: 0 description: The counts for (likely) pathogenic. uncertain_counts: type: array items: type: integer format: int32 minimum: 0 description: The counts for uncertain significance. benign_counts: type: array items: type: integer format: int32 minimum: 0 description: The counts for (likely) benign. GenesConditionsRecord: type: object description: Record from the integrated conditions computation. required: - hgnc_id - disease_associations - panelapp_associations properties: hgnc_id: type: string description: The HGNC ID. disease_associations: type: array items: $ref: '#/components/schemas/GenesDiseaseAssociation' description: The gene-disease associations. panelapp_associations: type: array items: $ref: '#/components/schemas/GenesPanelappAssociation' description: The PanelApp associations. GenesDbnsfpRecord: type: object description: Code for data from the dbNSFP database. required: - gene_name - gene_old_names - gene_other_names - ccds_id - refseq_id - mim_id - omim_id - pathway_biocarta_short - pathway_biocarta_full - pathway_consensus_path_db - pathway_kegg_id - pathway_kegg_full - function_description - disease_description - mim_phenotype_id - mim_disease - orphanet_disorder_id - orphanet_disorder - orphanet_association_type - trait_association_gwas - hpo_id - hpo_name - go_biological_process - go_cellular_component - go_molecular_function - tissue_specificity_uniprot - expression_egenetics - expression_gnf_atlas - interactions_intact - interactions_biogrid - interactions_consensus_path_db properties: gene_name: type: string description: Gene symbol from HGNC. ensembl_gene: type: - string - 'null' description: Ensembl gene id (from HGNC). chr: type: - string - 'null' description: Chromosome number (from HGNC). gene_old_names: type: array items: type: string description: Old gene symbol (from HGNC). gene_other_names: type: array items: type: string description: Other gene names (from HGNC). uniprot_acc: type: - string - 'null' description: Uniprot acc (from HGNC). uniprot_id: type: - string - 'null' description: Uniprot id (from HGNC). entrez_gene_id: type: - string - 'null' description: Uniprot id (from HGNC). ccds_id: type: array items: type: string description: CCDS id (from HGNC). refseq_id: type: array items: type: string description: Refseq gene id (from HGNC). ucsc_id: type: - string - 'null' description: UCSC gene id (from HGNC). mim_id: type: array items: type: string description: MIM gene id (from OMIM). omim_id: type: array items: type: string description: MIM gene id from OMIM. gene_full_name: type: - string - 'null' description: Gene full name (from HGNC). pathway_uniprot: type: - string - 'null' description: Pathway description from Uniprot. pathway_biocarta_short: type: array items: type: string description: Short name of the Pathway(s) the gene belongs to (from BioCarta). pathway_biocarta_full: type: array items: type: string description: Full name(s) of the Pathway(s) the gene belongs to (from BioCarta). pathway_consensus_path_db: type: array items: type: string description: Pathway(s) the gene belongs to (from ConsensusPathDB). pathway_kegg_id: type: array items: type: string description: ID(s) of the Pathway(s) the gene belongs to (from KEGG). pathway_kegg_full: type: array items: type: string description: Full name(s) of the Pathway(s) the gene belongs to (from KEGG). function_description: type: array items: type: string description: Function description of the gene (from Uniprot). disease_description: type: array items: type: string description: Disease(s) the gene caused or associated with (from Uniprot). mim_phenotype_id: type: array items: type: string description: MIM id(s) of the phenotype the gene caused or associated with (from Uniprot). mim_disease: type: array items: type: string description: MIM disease name(s) with MIM id(s) in \[\] (from Uniprot). orphanet_disorder_id: type: array items: type: string description: Orphanet Number of the disorder the gene caused or associated with. orphanet_disorder: type: array items: type: string description: Disorder name from Orphanet. orphanet_association_type: type: array items: type: string description: The type of association beteen the gene and the disorder in Orphanet. trait_association_gwas: type: array items: type: string description: Trait(s) the gene associated with (from GWAS catalog). hpo_id: type: array items: type: string description: ID of the mapped Human Phenotype Ontology. hpo_name: type: array items: type: string description: Name of the mapped Human Phenotype Ontology. go_biological_process: type: array items: type: string description: GO terms for biological process. go_cellular_component: type: array items: type: string description: GO terms for cellular component. go_molecular_function: type: array items: type: string description: GO terms for molecular function. tissue_specificity_uniprot: type: array items: type: string description: Tissue specificity description from Uniprot. expression_egenetics: type: array items: type: string description: Tissues/organs the gene expressed in (egenetics data from BioMart). expression_gnf_atlas: type: array items: type: string description: Tissues/organs the gene expressed in (GNF/Atlas data from BioMart). interactions_intact: type: array items: type: string description: The interacting genes from IntAct. interactions_biogrid: type: array items: type: string description: The interacting genes from BioGRID. interactions_consensus_path_db: type: array items: type: string description: The interacting genes from ConsensusPathDB. haploinsufficiency: type: - number - 'null' format: double description: |- Estimated probability of haploinsufficiency of the gene (from doi:10.1371/journal.pgen.1001154). hipred_score: type: - number - 'null' format: double description: |- Estimated probability of haploinsufficiency of the gene (from doi:10.1093/bioinformatics/btx028). hipred: type: - string - 'null' description: |- HIPred prediction of haploinsufficiency of the gene. Y(es) or N(o). (from doi:10.1093/bioinformatics/btx028). ghis: type: - number - 'null' format: double description: |- A score predicting the gene haploinsufficiency. The higher the score the more likely the gene is haploinsufficient (from doi: 10.1093/nar/gkv474). prec: type: - number - 'null' format: double description: |- Estimated probability that gene is a recessive disease gene (from DOI:10.1126/science.1215040). known_rec_info: type: - string - 'null' description: |- Known recessive status of the gene (from DOI:10.1126/science.1215040) "lof-tolerant = seen in homozygous state in at least one 1000G individual" "recessive = known OMIM recessive disease" (original annotations from DOI:10.1126/science.1215040). rvis_evs: type: - number - 'null' format: double description: |- Residual Variation Intolerance Score, a measure of intolerance of mutational burden, the higher the score the more tolerant to mutational burden the gene is. Based on EVS (ESP6500) data. from doi:10.1371/journal.pgen.1003709. rvis_percentile_evs: type: - number - 'null' format: double description: |- The percentile rank of the gene based on RVIS, the higher the percentile the more tolerant to mutational burden the gene is. Based on EVS (ESP6500) data. lof_fdr_exac: type: - number - 'null' format: double description: |- "A gene's corresponding FDR p-value for preferential LoF depletion among the ExAC population. Lower FDR corresponds with genes that are increasingly depleted of LoF variants." cited from RVIS document. rvis_exac: type: - number - 'null' format: double description: |- "ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six individual ethnic strata from ExAC." cited from RVIS document. rvis_percentile_exac: type: - number - 'null' format: double description: |- "Genome-Wide percentile for the new ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six individual ethnic strata from ExAC." cited from RVIS document. exac_pli: type: - number - 'null' format: double description: |- "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 data. exac_prec: type: - number - 'null' format: double description: |- "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 data. exac_pnull: type: - number - 'null' format: double description: |- "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 data. exac_nontcga_pli: type: - number - 'null' format: double description: |- "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 nonTCGA subset. exac_nontcga_prec: type: - number - 'null' format: double description: |- "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 nonTCGA subset. exac_nontcga_pnull: type: - number - 'null' format: double description: |- "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 nonTCGA subset. exac_nonpsych_pli: type: - number - 'null' format: double description: |- "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 nonpsych subset. exac_nonpsych_prec: type: - number - 'null' format: double description: |- "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 nonpsych subset. exac_nonpsych_pnull: type: - number - 'null' format: double description: |- "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 nonpsych subset/ gnomad_pli: type: - number - 'null' format: double description: |- "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on gnomAD 2.1 data. gnomad_prec: type: - number - 'null' format: double description: |- "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on gnomAD 2.1 data. gnomad_pnull: type: - number - 'null' format: double description: |- "the probability of being tolerant of both heterozygous and homozygous lof variants" based on gnomAD 2.1 data. exac_del_score: type: - number - 'null' format: double description: '"Winsorised deletion intolerance z-score" based on ExAC r0.3.1 CNV data.' exac_dup_score: type: - number - 'null' format: double description: '"Winsorised duplication intolerance z-score" based on ExAC r0.3.1 CNV data.' exac_cnv_score: type: - number - 'null' format: double description: '"Winsorised cnv intolerance z-score" based on ExAC r0.3.1 CNV data.' exac_cnv_flag: type: - string - 'null' description: |- "Gene is in a known region of recurrent CNVs mediated by tandem segmental duplications and intolerance scores are more likely to be biased or noisy." from ExAC r0.3.1 CNV release. gdi: type: - number - 'null' format: double description: |- gene damage index score, "a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population" from doi: 10.1073/pnas.1518646112. The higher the score the less likely the gene is to be responsible for monogenic diseases. gdi_phred: type: - number - 'null' format: double description: Phred-scaled GDI scores. gdp_all_disease_causing: type: - string - 'null' description: gene damage prediction (low/medium/high) by GDI for all diseases., gdp_all_mendelian: type: - string - 'null' description: gene damage prediction (low/medium/high) by GDI for all Mendelian diseases. gdp_all_mendelian_ad: type: - string - 'null' description: |- gene damage prediction (low/medium/high) by GDI for Mendelian autosomal dominant diseases. gdp_mendelian_ar: type: - string - 'null' description: |- gene damage prediction (low/medium/high) by GDI for Mendelian autosomal recessive diseases. gdp_pid: type: - string - 'null' description: |- gene damage prediction (low/medium/high) by GDI for all primary immunodeficiency diseases. gdp_pid_ad: type: - string - 'null' description: |- gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal dominant diseases. gdp_pid_ar: type: - string - 'null' description: |- gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal recessive diseases. gdp_cancer: type: - string - 'null' description: gene damage prediction (low/medium/high) by GDI for all cancer disease. gdb_cancer_rec: type: - string - 'null' description: gene damage prediction (low/medium/high) by GDI for cancer recessive disease. gdp_cancer_dom: type: - string - 'null' description: gene damage prediction (low/medium/high) by GDI for cancer dominant disease. loftool_score: type: - number - 'null' format: double description: |- A percentile score for gene intolerance to functional change. The lower the score the higher gene intolerance to functional change. For details see doi: 10.1093/bioinformatics/btv602. sorva_lof_maf_5_het_or_hom: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_maf_5_hom_or_comphet: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_maf_1_het_or_hom: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_maf_1_hom_or_comphet: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_or_mis_maf_5_het_or_hom: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_or_mis_maf_5_hom_or_comphet: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_or_mis_maf_1_het_or_hom: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. sorva_lof_or_mis_maf_1_hom_or_comphet: type: - number - 'null' format: double description: |- The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. essential_gene: type: - string - 'null' description: |- Essential ("E") or Non-essential phenotype-changing ("N") based on Mouse Genome Informatics database. from doi:10.1371/journal.pgen.1003484. essential_gene_crispr: type: - string - 'null' description: |- Essential ("E") or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from doi: 10.1126/science.aac7041. essential_gene_crispr2: type: - string - 'null' description: |- Essential ("E"), context-Specific essential ("S"), or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from essential_gene_gene_trap: type: - string - 'null' description: |- Essential ("E"), HAP1-Specific essential ("H"), KBM7-Specific essential ("K"), or Non-essential phenotype-changing ("N"), based on large scale mutagenesis experiments. from doi: 10.1126/science.aac7557. gene_indispensability_score: type: - number - 'null' format: double description: |- A probability prediction of the gene being essential. From doi:10.1371/journal.pcbi.1002886. gene_indispensability_pred: type: - string - 'null' description: Essential ("E") or loss-of-function tolerant ("N") based on Gene_indispensability_score. mgi_mouse_gene: type: - string - 'null' description: Homolog mouse gene name from MGI. mgi_mouse_phenotype: type: - string - 'null' description: Phenotype description for the homolog mouse gene from MGI. zfin_zebrafish_gene: type: - string - 'null' description: Homolog zebrafish gene name from ZFIN. zfin_zebrafish_structure: type: - string - 'null' description: Affected structure of the homolog zebrafish gene from ZFIN. zfin_zebrafish_phenotype_quality: type: - string - 'null' description: Phenotype description for the homolog zebrafish gene from ZFIN. zfin_zebrafish_phenotype_tag: type: - string - 'null' description: Phenotype tag for the homolog zebrafish gene from ZFIN" GenesDecipherHiRecord: type: object description: Decipher HI Predictions required: - hgnc_id - hgnc_symbol - p_hi - hi_index properties: hgnc_id: type: string description: HGNC identifier. hgnc_symbol: type: string description: Official HGNC gene symbol. p_hi: type: number format: double description: P(HI) prediction from DECIPHER HI. hi_index: type: number format: double description: Percent HI index. GenesDiseaseAssociation: type: object description: A gene-disease association. required: - hgnc_id - labeled_disorders - sources - confidence properties: hgnc_id: type: string description: The HGNC ID. labeled_disorders: type: array items: $ref: '#/components/schemas/GenesLabeledDisorder' description: The gene-disease association entries. disease_name: type: - string - 'null' description: Overall disease name. disease_definition: type: - string - 'null' description: Disease definition. sources: type: array items: $ref: '#/components/schemas/GenesDiseaseAssociationSource' description: The gene-disease association sources. confidence: $ref: '#/components/schemas/GenesDiseaseAssociationConfidenceLevel' description: Overall disease-gene association confidence level. GenesDiseaseAssociationConfidenceLevel: type: string description: Enumeration for confidence levels. enum: - High - Medium - Low GenesDiseaseAssociationEntryConfidenceLevel: type: string description: Enumeration for confidence levels. enum: - High - Medium - Low GenesDiseaseAssociationSource: type: string description: Enumeration for sources. enum: - Omim - Orphanet - Panelapp GenesDominoRecord: type: object description: Information from DOMINO. required: - gene_symbol - score properties: gene_symbol: type: string description: Gene symbol. score: type: number format: double description: The score. GenesEntityType: type: string description: Enumeration for entity types. enum: - Gene - Str - Region GenesExtractedVariantsPerRelease: type: object description: Extracted variants per release. required: - variants properties: release: type: - string - 'null' description: Release version. variants: type: array items: $ref: '#/components/schemas/ClinvarExtractedVcvRecord' description: Variants per gene. GenesFields: type: string description: The allowed fields to search in. enum: - hgnc_id - symbol - name - alias_symbol - alias_name - ensembl_gene_id - ncbi_gene_id GenesGeneData: type: object description: Gene identity information. properties: hgnc_id: type: - string - 'null' description: HGNC ID. hgnc_symbol: type: - string - 'null' description: HGNC gene symbol. gene_symbol: type: - string - 'null' description: Gene symbol. GenesGeneDiseaseAssociationEntry: type: object description: A gene-disease association entry. required: - source - confidence properties: source: $ref: '#/components/schemas/GenesDiseaseAssociationSource' description: The gene-disease association source. confidence: $ref: '#/components/schemas/GenesDiseaseAssociationEntryConfidenceLevel' description: The gene-disease association confidence level. GenesGeneImpact: type: string description: Enumeration with the variant consequence. enum: - Unspecified - ThreePrimeUtrVariant - FivePrimeUtrVariant - DownstreamTranscriptVariant - FrameshiftVariant - InframeIndel - StartLost - IntronVariant - MissenseVariant - NonCodingTranscriptVariant - StopGained - NoSequenceAlteration - SpliceAcceptorVariant - SpliceDonorVariant - StopLost - SynonymousVariant - UpstreamTranscriptVariant GenesGeneImpactCounts: type: object description: Entry for storing counts of `GeneImpact` and `ClinicalSignificance`. required: - hgnc_id - impact_counts properties: hgnc_id: type: string description: The gene HGNC ID. impact_counts: type: array items: $ref: '#/components/schemas/GenesImpactCounts' description: The impact counts. GenesGeneInfoRecord: type: object description: Information about a gene. required: - panelapp properties: acmg_sf: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord' description: Information from the ACMG secondary finding list. clingen: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesClingenDosageRecord' description: Information from ClinGen dosage curation. dbnsfp: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDbnsfpRecord' description: Information from dbNSFP. gnomad_constraints: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGnomadConstraintsRecord' description: Information from the gnomAD constraints database. hgnc: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesHgncRecord' description: Information from the HGNC database. ncbi: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesNcbiRecord' description: Information from the NCBI gene database (aka "Entrez"). omim: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesOmimRecord' description: Information about gene to OMIM term annotation, composed from clingen and HPO. orpha: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesOrphaRecord' description: Information about gene to Orphanet annotation, derived from Orphapacket. rcnv: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesRcnvRecord' description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022). shet: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesShetRecord' description: Information from the sHet score (Weghor et al., 2019) gtex: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGtexRecord' description: Information from GTEx data domino: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDominoRecord' description: Information from DOMINO. decipher_hi: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDecipherHiRecord' description: DECIPHER HI score. panelapp: type: array items: $ref: '#/components/schemas/GenesPanelAppRecord' description: GenomicsEngland PanelApp gene information. conditions: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesConditionsRecord' description: Conditions record. GenesGeneRecord: type: object description: Entry in the genes RocksDB database. required: - panelapp properties: acmg_sf: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord' description: Information from the ACMG secondary finding list. clingen: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesClingenDosageRecord' description: Information from ClinGen dosage curation. dbnsfp: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDbnsfpRecord' description: Information from dbNSFP. gnomad_constraints: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGnomadConstraintsRecord' description: Information from the gnomAD constraints database. hgnc: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesHgncRecord' description: Information from the HGNC database. ncbi: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesNcbiRecord' description: Information from the NCBI gene database (aka "Entrez"). omim: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesOmimRecord' description: Information about gene to OMIM term annotation, composed from clingen and HPO. orpha: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesOrphaRecord' description: Information about gene to Orphanet annotation, derived from Orphapacket. rcnv: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesRcnvRecord' description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022). shet: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesShetRecord' description: Information from the sHet score (Weghor et al., 2019) gtex: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGtexRecord' description: Information from GTEx data domino: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDominoRecord' description: Information from DOMINO. decipher_hi: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesDecipherHiRecord' description: DECIPHER HI score. panelapp: type: array items: $ref: '#/components/schemas/GenesPanelAppRecord' description: GenomicsEngland PanelApp gene information. conditions: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesConditionsRecord' description: Conditions record. GenesGnomadConstraintsRecord: type: object description: Code for data from the gnomAD constraints. required: - ensembl_gene_id - entrez_id - gene_symbol properties: ensembl_gene_id: type: string description: The Ensembl gene ID. entrez_id: type: string description: The NCBI gene ID. gene_symbol: type: string description: The HGNC gene symbol. exp_lof: type: - number - 'null' format: double description: The expected number of loss-of-function variants. exp_mis: type: - number - 'null' format: double description: The expected number of missense variants. exp_syn: type: - number - 'null' format: double description: The expected number of synonymous variants. mis_z: type: - number - 'null' format: double description: The missense-related Z-score. obs_lof: type: - integer - 'null' format: int32 description: The observed number of loss-of-function variants. minimum: 0 obs_mis: type: - integer - 'null' format: int32 description: The observed number of missense variants. minimum: 0 obs_syn: type: - integer - 'null' format: int32 description: The observed number of synonymous variants. minimum: 0 oe_lof: type: - number - 'null' format: double description: The loss-of-function observed/expected ratio. oe_lof_lower: type: - number - 'null' format: double description: The lower bound of the loss-of-function observed/expected ratio. oe_lof_upper: type: - number - 'null' format: double description: The upper bound of the loss-of-function observed/expected ratio. oe_mis: type: - number - 'null' format: double description: The missense observed/expected ratio. oe_mis_lower: type: - number - 'null' format: double description: The lower bound of the missense observed/expected ratio. oe_mis_upper: type: - number - 'null' format: double description: The upper bound of the missense observed/expected ratio. oe_syn: type: - number - 'null' format: double description: The synonymous observed/expected ratio. oe_syn_lower: type: - number - 'null' format: double description: The lower bound of the synonymous observed/expected ratio. oe_syn_upper: type: - number - 'null' format: double description: The upper bound of the synonymous observed/expected ratio. pli: type: - number - 'null' format: double description: The probability of loss-of-function intolerance (pLI score). syn_z: type: - number - 'null' format: double description: The synonymous-related Z-score. exac_pli: type: - number - 'null' format: double description: The probability of loss-of-function intolerance (pLI score) from ExAC. exac_obs_lof: type: - number - 'null' format: double description: The observed number of loss-of-function variants from ExAC. exac_exp_lof: type: - number - 'null' format: double description: The expected number of loss-of-function variants from ExAC. exac_oe_lof: type: - number - 'null' format: double description: The loss-of-function observed/expected ratio from ExAC. GenesGtexRecord: type: object description: Entry with the GTEx information. required: - hgnc_id - ensembl_gene_id - ensembl_gene_version - records properties: hgnc_id: type: string description: The HGNC ID. ensembl_gene_id: type: string description: ENSEMBL gene ID. ensembl_gene_version: type: string description: ENSEMBL gene version. records: type: array items: $ref: '#/components/schemas/GenesGtexTissueRecord' description: Counts per tissue GenesGtexTissue: type: string description: Enumeration for GTEx V8 tissue enum: - AdiposeTissue - AdrenalGland - Bladder - Blood - BloodVessel - BoneMarrow - Brain - Breast - CervixUteri - Colon - Esophagus - FallopianTube - Heart - Kidney - Liver - Lung - Muscle - Nerve - Ovary - Pancreas - Pituitary - Prostate - SalivaryGland - Skin - SmallIntestine - Spleen - Stomach - Testis - Thyroid - Uterus - Vagina GenesGtexTissueDetailed: type: string description: Enumeration for GTEx V8 tissue details enum: - AdiposeSubcutaneous - AdiposeVisceralOmentum - AdrenalGland - ArteryAorta - ArteryCoronary - ArteryTibial - Bladder - BrainAmygdala - BrainAnteriorCingulateCortex - BrainCaudateBasalGanglia - BrainCerebellarHemisphere - BrainCerebellum - BrainCortex - BrainFrontalCortex - BrainHippocampus - BrainHypothalamus - BrainNucleusAccumbens - BrainPutamenBasalGanglia - BrainSpinalCord - BrainSubstantiaNigra - BreastMammaryTissue - CellsCulturedFibroblasts - CellsEbvTransformedLymphocytes - CellsLeukemiaCellLine - CervixEctocervix - CervixEndocervix - ColonSigmoid - ColonTransverse - EsophagusGastroesophagealJunction - EsophagusMucosa - EsophagusMuscularis - FallopianTube - HeartAtrialAppendage - HeartLeftVentricle - KidneyCortex - KidneyMedulla - Liver - Lung - MinorSalivaryGland - MuscleSkeletal - NerveTibial - Ovary - Pancreas - Pituitary - Prostate - SalivaryGland - SkinNotSunExposedSuprapubic - SkinSunExposedLowerLeg - SmallIntestineTerminalIleum - Spleen - Stomach - Testis - Thyroid - Uterus - Vagina - WholeBlood GenesGtexTissueRecord: type: object description: Entry with the tissue-specific information for a gene. required: - tissue - tissue_detailed - tpms properties: tissue: $ref: '#/components/schemas/GenesGtexTissue' description: The tissue type tissue_detailed: $ref: '#/components/schemas/GenesGtexTissueDetailed' description: The detailed tissue type tpms: type: array items: type: number format: float description: TPM counts GenesHgncLsdb: type: object description: Information from the locus-specific dabase. required: - name - url properties: name: type: string description: The name of the Locus Specific Mutation Database. url: type: string description: The URL for the gene. GenesHgncRecord: type: object description: A record from the HGNC database. required: - hgnc_id - symbol - name - status - alias_symbol - alias_name - prev_symbol - prev_name - gene_group - gene_group_id - ena - refseq_accession - ccds_id - uniprot_ids - pubmed_id - mgd_id - rgd_id - lsdb - omim_id - enzyme_id - mane_select properties: hgnc_id: type: string description: HGNC ID. A unique ID created by the HGNC for every approved symbol. symbol: type: string description: The HGNC approved gene symbol. name: type: string description: HGNC approved name for the gene. locus_group: type: - string - 'null' description: |- A group name for a set of related locus types as defined by the HGNC (e.g. non-coding RNA). locus_type: type: - string - 'null' description: The locus type as defined by the HGNC (e.g. RNA, transfer). status: type: integer format: int32 description: Status of the symbol report. location: type: - string - 'null' description: Cytogenetic location of the gene (e.g. 2q34). location_sortable: type: - string - 'null' description: Sortable cytogenic location of the gene (e.g. 02q34). alias_symbol: type: array items: type: string description: Other symbols used to refer to this gene. alias_name: type: array items: type: string description: Other names used to refer to this gene. prev_symbol: type: array items: type: string description: Prevous symbols used to refer to this gene. prev_name: type: array items: type: string description: Previous names used to refer to this gene. gene_group: type: array items: type: string description: Name given to a gene group. gene_group_id: type: array items: type: integer format: int32 minimum: 0 description: ID used to designate a gene group. date_approved_reserved: type: - string - 'null' description: The date the entry was first approved. date_symbol_changed: type: - string - 'null' description: The date the gene symbol was last changed. date_name_changed: type: - string - 'null' description: The date the gene name was last changed. date_modified: type: - string - 'null' description: Date the entry was last modified. entrez_id: type: - string - 'null' description: Entrez gene id. ensembl_gene_id: type: - string - 'null' description: Ensembl gene id. vega_id: type: - string - 'null' description: Vega gene id. ucsc_id: type: - string - 'null' description: UCSC gene id. ena: type: array items: type: string description: ENA accession number(s). refseq_accession: type: array items: type: string description: RefSeq nucleotide accession(s). ccds_id: type: array items: type: string description: Consensus CDS ID(ds). uniprot_ids: type: array items: type: string description: Uniprot IDs. pubmed_id: type: array items: type: integer format: int32 minimum: 0 description: Pubmed IDs. mgd_id: type: array items: type: string description: Mouse genome informatics database ID(s). rgd_id: type: array items: type: string description: Rat genome database gene ID(s). lsdb: type: array items: $ref: '#/components/schemas/GenesHgncLsdb' description: The name of the Locus Specific Mutation Database and URL for the gene. cosmic: type: - string - 'null' description: Symbol used within COSMIC. omim_id: type: array items: type: string description: OMIM ID(s). mirbase: type: - string - 'null' description: miRBase ID. homeodb: type: - integer - 'null' format: int32 description: Homeobox Database ID. minimum: 0 snornabase: type: - string - 'null' description: snoRNABase ID. bioparadigms_slc: type: - string - 'null' description: |- Symbol used to link to the SLC tables database at bioparadigms.org for the gene. orphanet: type: - integer - 'null' format: int32 description: Orphanet ID. minimum: 0 pseudogene_org: type: - string - 'null' description: Pseudogene.org. horde_id: type: - string - 'null' description: Symbol used within HORDE for the gene. merops: type: - string - 'null' description: ID used to link to the MEROPS peptidase database. imgt: type: - string - 'null' description: Symbol used within international ImMunoGeneTics information system. iuphar: type: - string - 'null' description: |- The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY database. cd: type: - string - 'null' description: Symbol used within the Human Cell Differentiation Molecule database. mamit_trnadb: type: - integer - 'null' format: int32 description: ID to link to the Mamit-tRNA database minimum: 0 lncrnadb: type: - string - 'null' description: lncRNA Database ID. enzyme_id: type: array items: type: string description: ENZYME EC accession number. intermediate_filament_db: type: - string - 'null' description: ID used to link to the Human Intermediate Filament Database. agr: type: - string - 'null' description: The HGNC ID that the Alliance of Genome Resources (AGR) use. mane_select: type: array items: type: string description: |- NCBI and Ensembl transcript IDs/acessions including the version number. GenesHgncStatus: type: string description: Status of the symbol report, which can be either "Approved" or "Entry Withdrawn". enum: - Approved - Withdrawn GenesImpactCounts: type: object description: Stores the counts for a gene impact. required: - gene_impact - count_benign - count_likely_benign - count_uncertain_significance - count_likely_pathogenic - count_pathogenic properties: gene_impact: $ref: '#/components/schemas/GenesGeneImpact' description: The gene impact. count_benign: type: integer format: int32 description: The counts for the benign impact. minimum: 0 count_likely_benign: type: integer format: int32 description: The counts for the likely benign impact. minimum: 0 count_uncertain_significance: type: integer format: int32 description: The counts for the uncertain significance impact. minimum: 0 count_likely_pathogenic: type: integer format: int32 description: The counts for the likely pathogenic impact. minimum: 0 count_pathogenic: type: integer format: int32 description: The counts for the pathogenic impact. minimum: 0 GenesInfoResponse: type: object description: Query response for `handle_with_openapi()`. required: - genes properties: genes: type: array items: $ref: '#/components/schemas/GenesGeneInfoRecord' description: Version information of the genes. GenesLabeledDisorder: type: object description: A labeled disorder. required: - term_id properties: term_id: type: string description: The disorder ID. title: type: - string - 'null' description: The disorder name. GenesLookupResponse: type: object description: Result for `async fn handle_with_openapi( required: - genes properties: genes: type: array items: $ref: '#/components/schemas/GenesLookupResultEntry' description: The resulting gene information. GenesLookupResultEntry: type: object description: One result entry in the response. required: - query properties: query: type: string description: The query string, gene_names: oneOf: - type: 'null' - $ref: '#/components/schemas/GeneNames' description: The gene names information. GenesNcbiRecord: type: object description: A record from the NCBI gene database. required: - gene_id - rif_entries properties: gene_id: type: string description: NCBI Gene ID. summary: type: - string - 'null' description: Gene summary. rif_entries: type: array items: $ref: '#/components/schemas/GenesRifEntry' description: '"Reference Into Function" entry.' GenesOmimRecord: type: object description: A record from the OMIM gene association. required: - hgnc_id - omim_diseases properties: hgnc_id: type: string description: The HGNC gene ID. omim_diseases: type: array items: $ref: '#/components/schemas/GenesOmimTerm' description: The associated OMIM records. GenesOmimTerm: type: object description: Description of an OMIM record. required: - omim_id - label properties: omim_id: type: string description: The OMIM ID. label: type: string description: The OMIM label. GenesOrphaRecord: type: object description: A record from the ORDO gene association. required: - hgnc_id - orpha_diseases properties: hgnc_id: type: string description: The HGNC gene ID. orpha_diseases: type: array items: $ref: '#/components/schemas/GenesOrphaTerm' description: The associated ORPHA diseases. GenesOrphaTerm: type: object description: Description of an ORDO record. required: - orpha_id - label properties: orpha_id: type: string description: The ORPHA ID. label: type: string description: The disease name. GenesPanel: type: object description: Message for panel information. required: - id - name - disease_group - disease_sub_group - version - version_created - relevant_disorders - types properties: id: type: integer format: int32 description: Panel ID. minimum: 0 hash_id: type: - string - 'null' description: Panel hash ID. name: type: string description: Panel name. disease_group: type: string description: Disease group. disease_sub_group: type: string description: Disease subgroup. version: type: string description: Version version_created: type: string description: Creation date of version. relevant_disorders: type: array items: type: string description: Relevant disorders. stats: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesPanelStats' description: Stats. types: type: array items: $ref: '#/components/schemas/GenesPanelType' description: Panel types. GenesPanelAppRecord: type: object description: Entry in PanelApp. required: - entity_type - entity_name - confidence_level - publications - evidence - phenotypes - mode_of_inheritance properties: gene_data: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesGeneData' description: Gene identity information. entity_type: $ref: '#/components/schemas/GenesEntityType' description: Entity type. entity_name: type: string description: Entity name. confidence_level: $ref: '#/components/schemas/GenesPanelappRecordConfidenceLevel' description: Confidence level. penetrance: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesPenetrance' description: Penetrance. publications: type: array items: type: string description: Publications. evidence: type: array items: type: string description: Evidence. phenotypes: type: array items: type: string description: Phenotypes. mode_of_inheritance: type: string description: Mode of inheritance. panel: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesPanel' description: Panel. GenesPanelStats: type: object description: Message for panel statistics. required: - number_of_genes - number_of_strs - number_of_regions properties: number_of_genes: type: integer format: int32 description: Number of genes. minimum: 0 number_of_strs: type: integer format: int32 description: Number of STRs. minimum: 0 number_of_regions: type: integer format: int32 description: Number of regions. minimum: 0 GenesPanelType: type: object description: Message for panel types. required: - name - slug - description properties: name: type: string description: Type name. slug: type: string description: Slug. description: type: string description: Description. GenesPanelappAssociation: type: object description: An association of a gene by HGNC with a panel from PanelApp. required: - hgnc_id - confidence_level - entity_type - phenotypes properties: hgnc_id: type: string description: The HGNC ID. confidence_level: $ref: '#/components/schemas/GenesPanelappAssociationConfidenceLevel' description: The PanelApp confidence level. entity_type: $ref: '#/components/schemas/GenesPanelappEntityType' description: The PanelApp entity type. mode_of_inheritance: type: - string - 'null' description: The PanelApp entity name. phenotypes: type: array items: type: string description: The PanelApp publications. panel: oneOf: - type: 'null' - $ref: '#/components/schemas/GenesPanelappPanel' description: The PanelApp panel. GenesPanelappAssociationConfidenceLevel: type: string description: Enumeration for PanelApp confidence level. enum: - Green - Amber - Red - None GenesPanelappEntityType: type: string description: Enumeration for entity type. enum: - Gene - Region - Str GenesPanelappPanel: type: object description: A panel from PanelApp. required: - id - name - version properties: id: type: integer format: int32 description: PanelApp panel ID. name: type: string description: PanelApp panel name. version: type: string description: PanelApp panel version. GenesPanelappRecordConfidenceLevel: type: string description: Enumeration for PanelApp confidence level. enum: - Green - Amber - Red - None GenesPenetrance: type: string description: Enumeration for penetrance. enum: - Complete - Incomplete GenesRcnvRecord: type: object description: Entry in the rCNV dosage sensitivity scores (Collins et al., 2022). required: - hgnc_id - p_haplo - p_triplo properties: hgnc_id: type: string description: The HGNC ID. p_haplo: type: number format: double description: The pHaplo value. p_triplo: type: number format: double description: The pTriplo value. GenesRifEntry: type: object description: Reference into function record. required: - text - pmids properties: text: type: string description: The RIF text. pmids: type: array items: type: integer format: int32 minimum: 0 description: PubMed IDs. GenesSearchQuery: type: object description: Parameters for `handle`. required: - q properties: q: type: string description: The string to search for. fields: type: - array - 'null' items: $ref: '#/components/schemas/GenesFields' description: The fields to search in. case_sensitive: type: - boolean - 'null' description: Enable case sensitive search. GenesSearchResponse: type: object description: Result for `handle`. required: - genes properties: genes: type: array items: $ref: '#/components/schemas/Scored' description: The resulting gene information. GenesShetRecord: type: object description: Entry with sHet information (Weghorn et al., 2019). required: - hgnc_id - s_het properties: hgnc_id: type: string description: The HGNC ID. s_het: type: number format: double description: The sHet value. GenomeRelease: type: string description: Local genome release for command line arguments. enum: - grch37 - grch38 Gnomad2AgeInfo: type: object description: Encapsulate VCF INFO fields related to age. required: - age_hist_hom_bin_freq - age_hist_het_bin_freq properties: age_hist_hom_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]. age_hist_hom_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a homoplasmic variant. age_hist_hom_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a homoplasmic variant. age_hist_het_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0] age_hist_het_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a heteroplasmic variant. age_hist_het_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a heteroplasmic variant. Gnomad2AlleleCounts: type: object description: Store the relevant allele counts and frequencies in a given sub cohort. required: - ac - an - nhomalt - af properties: ac: type: integer format: int32 description: Number of alternate alleles in sub cohort. an: type: integer format: int32 description: Total number of alleles in the sub cohort. nhomalt: type: integer format: int32 description: Number of homozygous alternate alleles in the sub cohort. af: type: number format: float description: Alternate allele frequency in the sub cohort. Gnomad2AlleleCountsBySex: type: object description: Store the allele counts for the given sub cohort and sub cohort factored by sex. properties: overall: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCounts' description: Overall allele counts in the sub cohort. xx: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCounts' description: Allele counts in female/XX karyotype individuals of sub cohort. xy: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCounts' description: Allele counts in male/XY karyotype individuals of sub cohort. Gnomad2CohortAlleleCounts: type: object description: Store the allele counts for the given cohort. required: - by_population properties: cohort: type: - string - 'null' description: Name of the cohort. by_population: type: array items: $ref: '#/components/schemas/Gnomad2PopulationAlleleCounts' description: Allele counts for each population. by_sex: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCountsBySex' description: Allele counts by sex. raw: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCounts' description: Raw allele counts. popmax: type: - string - 'null' description: The population with maximum AF. af_popmax: type: - number - 'null' format: float description: |- Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry). ac_popmax: type: - integer - 'null' format: int32 description: Allele count in population with maximum AF. an_popmax: type: - integer - 'null' format: int32 description: Total number of alleles in population with maximum AF. nhomalt_popmax: type: - integer - 'null' format: int32 description: Total number of homozygous individuals in population with maximum AF. Gnomad2DepthInfo: type: object description: Encapsulate VCF INFO fields related to depth. required: - dp_hist_all_bin_freq - dp_hist_alt_bin_freq properties: dp_hist_all_n_larger: type: - integer - 'null' format: int32 description: Count of dp values falling above highest histogram bin edge for all individuals. dp_hist_alt_n_larger: type: - integer - 'null' format: int32 description: |- Count of dp values falling above highest histogram bin edge for individuals with the alternative allele dp_hist_all_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] dp_hist_alt_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] Gnomad2Filter: type: string description: Protocol buffer enum for site-level filters. enum: - allele_count_is_zero - inbreeding_coeff - pass - random_forest Gnomad2LiftoverInfo: type: object description: Liftover related information. required: - reverse_complemented_alleles - swapped_alleles - original_alleles properties: reverse_complemented_alleles: type: boolean description: |- The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the previous reference to the current one was on the negative strand. swapped_alleles: type: boolean description: |- The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It is possible that not all INFO annotations reflect this swap, and in the genotypes, only the GT, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that was used during the LiftOver to be sure. original_alleles: type: array items: type: string description: |- A list of the original alleles (including REF) of the variant prior to liftover. If the alleles were not changed during liftover, this attribute will be omitted. original_contig: type: - string - 'null' description: The name of the source contig/chromosome prior to liftover. original_start: type: - string - 'null' description: The position of the variant on the source contig prior to liftover. Gnomad2PopulationAlleleCounts: type: object description: Store the allele counts for the given population. required: - population properties: population: type: string description: Name of the population. counts: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AlleleCountsBySex' description: The overall allele counts and the one by sex. faf95: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 95% CI). faf99: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 99% CI). Gnomad2QualityInfo: type: object description: Encapsulate quality-related information. required: - vqsr_positive_train_site - vqsr_negative_train_site - segdup - lcr - decoy - transmitted_singleton properties: fs: type: - number - 'null' format: float description: Phred-scaled p-value of Fisher's exact test for strand bias. inbreeding_coeff: type: - number - 'null' format: float description: |- Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation. mq: type: - number - 'null' format: float description: Root mean square of the mapping quality of reads across all samples. mq_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference read mapping qualities. qd: type: - number - 'null' format: float description: Variant call confidence normalized by depth of sample reads supporting a variant. read_pos_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference read position bias. vqsr_positive_train_site: type: boolean description: Variant was used to build the positive training set of high-quality variants for VQSR. vqsr_negative_train_site: type: boolean description: Variant was used to build the negative training set of low-quality variants for VQSR. base_q_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference base qualities. clipping_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference number of hard clipped bases. sor: type: - number - 'null' format: float description: Strand bias estimated by the symmetric odds ratio test dp: type: - integer - 'null' format: int32 description: |- Depth of informative coverage for each sample; reads with MQ=255 or with bad mates are filtered. vqslod: type: - number - 'null' format: float description: |- Log-odds ratio of being a true variant versus being a false positive under the trained VQSR Gaussian mixture model. vqsr_culprit: type: - string - 'null' description: Allele-specific worst-performing annotation in the VQSR Gaussian mixture model segdup: type: boolean description: Variant falls within a segmental duplication region lcr: type: boolean description: Variant falls within a low complexity region. decoy: type: boolean description: Variant falls within a reference decoy region. transmitted_singleton: type: boolean description: |- Variant was a callset-wide doubleton that was transmitted within a family (i.e., a singleton amongst unrelated sampes in cohort). pab_max: type: - number - 'null' format: float description: |- Maximum p-value over callset for binomial test of observed allele balance for a heterozygous genotype, given expectation of AB=0.5. Gnomad2RandomForestInfo: type: object description: Random forest related information. required: - rf_tp_probability - rf_positive_label - rf_negative_label - rf_train properties: rf_tp_probability: type: number format: float description: Random forest prediction probability for a site being a true variant. rf_positive_label: type: boolean description: Variant was labelled as a positive example for training of random forest model. rf_negative_label: type: boolean description: Variant was labelled as a negative example for training of random forest model. rf_label: type: - string - 'null' description: Random forest training label. rf_train: type: boolean description: Variant was used in training random forest model. Gnomad2Record: type: object description: |- Protocol buffer for the gnomAD v2 VCF record. The more specialized fields from the INFO column are stored in separate, optional fields such that we don't end up with a humongous message. required: - chrom - pos - ref_allele - alt_allele - filters - vep - allele_counts - nonpar properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: Alternate allele. filters: type: array items: $ref: '#/components/schemas/Gnomad2Filter' description: Site-level filters. vep: type: array items: $ref: '#/components/schemas/Gnomad2Vep' description: VEP annotation records. allele_counts: type: array items: $ref: '#/components/schemas/Gnomad2CohortAlleleCounts' description: |- Variant allele counts in the different cohorts and population. The populations in gnomAD v2/3 are: empty for global, "controls", "non_cancer", "non_neuro", and "non_topmed". nonpar: type: boolean description: Variant (on sex chromosome) falls outside a pseudoautosomal region liftover_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2LiftoverInfo' description: Information on lift-over from GRCh37 to GRCh38. rf_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2RandomForestInfo' description: Random forest related information. variant_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2VariantInfo' description: Variant-related information details. quality_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2QualityInfo' description: Summary information for variant quality interpretation. age_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2AgeInfo' description: Age-related information. depth_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad2DepthInfo' description: Depth of coverage-related information. Gnomad2VariantInfo: type: object description: Variant type related information. required: - variant_type - allele_type - n_alt_alleles - was_mixed - has_star properties: variant_type: type: string description: Variant type (snv, indel, multi-snv, multi-indel, or mixed). allele_type: type: string description: Allele type (snv, ins, del, or mixed). n_alt_alleles: type: integer format: int32 description: Total number of alternate alleles observed at variant locus. was_mixed: type: boolean description: Variant type was mixed. has_star: type: boolean description: |- Variant locus coincides with a spanning deletion (represented by a star) observed elsewhere in the callset. Gnomad2Vep: type: object description: Protocol buffer for the gnomAD-mtDNA VEP predictions. required: - allele - consequence - impact - symbol - gene - feature_type - feature - feature_biotype - canonical - domains properties: allele: type: string description: Allele of record. consequence: type: string description: Consequence, e.g., `"missense_variant"`. impact: type: string description: Impact, e.g., `"MODERATE"`. symbol: type: string description: Gene symbol, e.g., `"PCSK9"`. gene: type: string description: Gene ID, `e.g., "ENSG00000169174"`. feature_type: type: string description: Feature type, e.g., `"Transcript"`. feature: type: string description: Feature ID, e.g., `"ENST00000302118"`. feature_biotype: type: string description: Feature biotype, e.g., `"protein_coding"`. exon: type: - string - 'null' description: Ranked exon number, e.g., `"1/4"`. intron: type: - string - 'null' description: Ranked intron number, e.g., `"1/4"`. hgvsc: type: - string - 'null' description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`. hgvsp: type: - string - 'null' description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`. cdna_position: type: - string - 'null' description: cDNA position, e.g., `"89/1863"`. cds_position: type: - string - 'null' description: CDS position, e.g., `"89/1863"`. protein_position: type: - string - 'null' description: Protein position, e.g., `"30/620"`. amino_acids: type: - string - 'null' description: Amino acids, e.g., `"T/R"`. codons: type: - string - 'null' description: Codons, e.g., `"gCg/gGg"`. existing_variation: type: - string - 'null' description: Existing variation info. dbsnp_id: type: - string - 'null' description: dbSNP ID, e.g., `"rs28942080"`. distance: type: - string - 'null' description: Distance output of VEP. strand: type: - string - 'null' description: Strand, e.g., `"1"`. flags: type: - string - 'null' description: Flags, e.g., `"cds_end_NF"`. variant_class: type: - string - 'null' description: Variant class, e.g., `"SNV"`. minimised: type: - string - 'null' description: Minimised output of VEP. symbol_source: type: - string - 'null' description: Symbol source, e.g., `"HGNC"`. hgnc_id: type: - string - 'null' description: HGNC ID, e.g., `"HGNC:8706"`. canonical: type: boolean description: Whether this is the canonical transcript. tsl: type: - integer - 'null' format: int32 description: Transcript support level, e.g., `"1"`. appris: type: - string - 'null' description: APPRIS annotation, e.g. `"P1"`. ccds: type: - string - 'null' description: CCDS ID, e.g., `"CCDS30547.1"`. ensp: type: - string - 'null' description: Ensembl protein ID, e.g., `"ENSP00000302118"`. swissprot: type: - string - 'null' description: SwissProt ID, e.g., `"P04114"`. trembl: type: - string - 'null' description: TREMBL ID, e.g., `"Q5T4W7"`. uniparc: type: - string - 'null' description: UniParc ID, e.g., `"UPI000002D4B2"`. gene_pheno: type: - string - 'null' description: Gene phenotype from VEP. sift: oneOf: - type: 'null' - $ref: '#/components/schemas/VepCommonPrediction' description: SIFT prediction, e.g., `"tolerated(0.06)"`. polyphen: oneOf: - type: 'null' - $ref: '#/components/schemas/VepCommonPrediction' description: PolyPhen prediction, e.g., `"benign(0.001)"`. domains: type: array items: $ref: '#/components/schemas/VepCommonDomain' description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`. hgvs_offset: type: - string - 'null' description: HGVS offset. gmaf: type: - number - 'null' format: float description: Overall minor allele frequency. afr_maf: type: - number - 'null' format: float description: Minor allele frequency in AFR population. amr_maf: type: - number - 'null' format: float description: Minor allele frequency in AMR population. eas_maf: type: - number - 'null' format: float description: Minor allele frequency in EAS population. eur_maf: type: - number - 'null' format: float description: Minor allele frequency in EUR population. sas_maf: type: - number - 'null' format: float description: Minor allele frequency in SAS population. aa_maf: type: - number - 'null' format: float description: Minor allele frequency in AA population. ea_maf: type: - number - 'null' format: float description: Minor allele frequency in EA population. exac_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC. exac_adj_maf: type: - number - 'null' format: float description: Minor allele frequency EXAC ADJ population. exac_afr_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC AFR population. exac_amr_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC AMR population. exac_eas_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC EAS population. exac_fin_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC FIN population. exac_nfe_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC NFE population. exac_oth_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC OTH population. exac_sas_maf: type: - number - 'null' format: float description: Minor allele frequency in ExAC SAS population. clin_sig: type: - string - 'null' description: Clinical significance. somatic: type: - string - 'null' description: Whether the variant is somatic. pheno: type: - string - 'null' description: Phenotype. pubmed: type: - string - 'null' description: Pubmed ID. motif_name: type: - string - 'null' description: Motif name. motif_pos: type: - string - 'null' description: Motif pos. high_inf_pos: type: - string - 'null' description: '"high inf pos" from VEP.' motif_score_change: type: - string - 'null' description: Motif score change. lof: type: - string - 'null' description: Loss of function prediction. lof_filter: type: - string - 'null' description: Loss of function filter. lof_flags: type: - string - 'null' description: Loss of function flags. lof_info: type: - string - 'null' description: Loss of function info. Gnomad3AgeInfo: type: object description: Encapsulate VCF INFO fields related to age. required: - age_hist_hom_bin_freq - age_hist_het_bin_freq properties: age_hist_hom_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]. age_hist_hom_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a homoplasmic variant. age_hist_hom_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a homoplasmic variant. age_hist_het_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0] age_hist_het_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a heteroplasmic variant. age_hist_het_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a heteroplasmic variant. Gnomad3AlleleCounts: type: object description: Store the relevant allele counts and frequencies in a given sub cohort. required: - ac - an - nhomalt - af properties: ac: type: integer format: int32 description: Number of alternate alleles in sub cohort. an: type: integer format: int32 description: Total number of alleles in the sub cohort. nhomalt: type: integer format: int32 description: Number of homozygous alternate alleles in the sub cohort. af: type: number format: float description: Alternate allele frequency in the sub cohort. Gnomad3AlleleCountsBySex: type: object description: Store the allele counts for the given sub cohort and sub cohort factored by sex. properties: overall: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCounts' description: Overall allele counts in the sub cohort. xx: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCounts' description: Allele counts in female/XX karyotype individuals of sub cohort. xy: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCounts' description: Allele counts in male/XY karyotype individuals of sub cohort. Gnomad3CohortAlleleCounts: type: object description: Store the allele counts for the given cohort. required: - by_population properties: cohort: type: - string - 'null' description: Name of the cohort. by_population: type: array items: $ref: '#/components/schemas/Gnomad3PopulationAlleleCounts' description: Allele counts for each population. by_sex: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCountsBySex' description: Allele counts by sex. raw: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCounts' description: Raw allele counts. popmax: type: - string - 'null' description: The population with maximum AF. af_popmax: type: - number - 'null' format: float description: |- Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry). ac_popmax: type: - integer - 'null' format: int32 description: Allele count in population with maximum AF. an_popmax: type: - integer - 'null' format: int32 description: Total number of alleles in population with maximum AF. nhomalt_popmax: type: - integer - 'null' format: int32 description: Total number of homozygous individuals in population with maximum AF. Gnomad3DepthInfo: type: object description: Encapsulate VCF INFO fields related to depth. required: - dp_hist_all_bin_freq - dp_hist_alt_bin_freq properties: dp_hist_all_n_larger: type: - integer - 'null' format: int32 description: Count of dp values falling above highest histogram bin edge for all individuals. dp_hist_alt_n_larger: type: - integer - 'null' format: int32 description: |- Count of dp values falling above highest histogram bin edge for individuals with the alternative allele dp_hist_all_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] dp_hist_alt_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] Gnomad3EffectInfo: type: object description: Store details on variant effect predictions. properties: primate_ai_score: type: - number - 'null' format: float description: PrimateAI's deleteriousness score from 0 (less deleterious) to 1 (more deleterious). revel_score: type: - number - 'null' format: float description: |- dbNSFP's Revel score from 0 to 1. Variants with higher scores are predicted to be more likely to be deleterious. splice_ai_max_ds: type: - number - 'null' format: float description: |- Illumina's SpliceAI max delta score; interpreted as the probability of the variant being splice-altering. splice_ai_consequence: type: - string - 'null' description: The consequence term associated with the max delta score in 'splice_ai_max_ds'. cadd_raw: type: - number - 'null' format: float description: Raw CADD scores are interpretable as the extent to which the annotation profile for a given variant suggests that the variant is likely to be 'observed' (negative values) vs 'simulated' (positive values). Larger values are more deleterious. cadd_phred: type: - number - 'null' format: float description: Cadd Phred-like scores ('scaled C-scores') ranging from 1 to 99, based on the rank of each variant relative to all possible 8.6 billion substitutions in the human reference genome. Larger values are more deleterious. Gnomad3Filter: type: string description: Protocol buffer enum for site-level filters. enum: - allele_count_is_zero - as_vsqr - inbreeding_coeff - pass Gnomad3PopulationAlleleCounts: type: object description: Store the allele counts for the given sub cohort in the given population. required: - population properties: population: type: string description: Name of the population. counts: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCountsBySex' description: The overall allele counts and the one by sex. faf95: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 95% CI). faf99: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 99% CI). faf95_xx: type: - number - 'null' format: float description: The filtering allele frequency for XX samples (using Poisson 95% CI). faf99_xx: type: - number - 'null' format: float description: The filtering allele frequency for XX samples (using Poisson 99% CI). faf95_xy: type: - number - 'null' format: float description: The filtering allele frequency for XY samples (using Poisson 95% CI). faf99_xy: type: - number - 'null' format: float description: The filtering allele frequency for XY samples (using Poisson 99% CI). Gnomad3QualityInfo: type: object description: Encapsulate quality-related information. required: - positive_train_site - negative_train_site - segdup - lcr - transmitted_singleton properties: as_fs: type: - number - 'null' format: float description: Allele-specific phred-scaled p-value of Fisher's exact test for strand bias. inbreeding_coeff: type: - number - 'null' format: float description: |- Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation. as_mq: type: - number - 'null' format: float description: Allele-specific root mean square of the mapping quality of reads across all samples mq_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference read mapping qualities. as_mq_rank_sum: type: - number - 'null' format: float description: |- Allele-specific z-score from Wilcoxon rank sum test of alternate vs. reference read mapping qualities. as_qd: type: - number - 'null' format: float description: |- Allele-specific variant call confidence normalized by depth of sample reads supporting a variant. read_pos_rank_sum: type: - number - 'null' format: float description: Z-score from Wilcoxon rank sum test of alternate vs. reference read position bias. as_read_pos_rank_sum: type: - number - 'null' format: float description: Allele-specific z-score from Wilcoxon rank sum test of alternate vs. reference read position bias. as_sor: type: - number - 'null' format: float description: Allele-specific strand bias estimated by the symmetric odds ratio test. positive_train_site: type: boolean description: Variant was used to build the positive training set of high-quality variants for VQSR. negative_train_site: type: boolean description: Variant was used to build the negative training set of low-quality variants for VQSR. as_vqslod: type: - number - 'null' format: float description: Allele-specific log-odds ratio of being a true variant versus being a false positive under the trained VQSR Gaussian mixture model. as_culprit: type: - string - 'null' description: Allele-specific worst-performing annotation in the VQSR Gaussian mixture model. segdup: type: boolean description: Variant falls within a segmental duplication region. lcr: type: boolean description: Variant falls within a low complexity region. transmitted_singleton: type: boolean description: |- Variant was a callset-wide doubleton that was transmitted within a family (i.e., a singleton amongst unrelated sampes in cohort). as_pab_max: type: - number - 'null' format: float description: Maximum p-value over callset for binomial test of observed allele balance for a heterozygous genotype, given expectation of 0.5. as_qual_approx: type: - integer - 'null' format: int32 description: Allele-specific sum of PL\[0\] values; used to approximate the QUAL score. as_sb_table: type: - string - 'null' description: Allele-specific forward/reverse read counts for strand bias tests. sor: type: - number - 'null' format: float description: Strand bias estimated by the symmetric odds ratio test (v4 only). Gnomad3Record: type: object description: |- Protocol buffer for the gnomAD-nuclear VCF record. The more specialized fields from the INFO column are stored in separate, optional fields such that we don't end up with a humongous message. required: - chrom - pos - ref_allele - alt_allele - filters - vep - allele_counts - nonpar properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: Alternate allele. filters: type: array items: $ref: '#/components/schemas/Gnomad3Filter' description: Site-level filters. vep: type: array items: $ref: '#/components/schemas/Gnomad3Vep' description: VEP annotation records. allele_counts: type: array items: $ref: '#/components/schemas/Gnomad3CohortAlleleCounts' description: |- Variant allele counts in the different cohorts and population. The populations in gnomAD v2/3 are: empty for global, "controls", "non_cancer", "non_neuro", and "non_topmed". nonpar: type: boolean description: Variant (on sex chromosome) falls outside a pseudoautosomal region effect_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3EffectInfo' description: Information on variant scores. variant_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3VariantInfo' description: Variant-related information details. quality_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3QualityInfo' description: Summary information for variant quality interpretation. age_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AgeInfo' description: Age-related information. depth_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3DepthInfo' description: Depth of coverage-related information. Gnomad3VariantInfo: type: object description: Variant type related information. required: - variant_type - allele_type - n_alt_alleles - was_mixed - monoallelic - var_dp properties: variant_type: type: string description: Variant type (snv, indel, multi-snv, multi-indel, or mixed). allele_type: type: string description: Allele type (snv, ins, del, or mixed). n_alt_alleles: type: integer format: int32 description: Total number of alternate alleles observed at variant locus. was_mixed: type: boolean description: Variant type was mixed. monoallelic: type: boolean description: All samples are homozygous alternate for the variant. var_dp: type: integer format: int32 description: Depth over variant genotypes (does not include depth of reference samples). as_vardp: type: - integer - 'null' format: int32 description: Allele-specific depth over variant genotypes (does not include depth of reference samples) (v4 only). Gnomad3Vep: type: object description: Protocol buffer for the gnomAD-nuclear VEP predictions. required: - allele - consequence - impact - symbol - gene - feature_type - feature - feature_biotype - domains properties: allele: type: string description: Allele of record. consequence: type: string description: Consequence, e.g., `"missense_variant"`. impact: type: string description: Impact, e.g., `"MODERATE"`. symbol: type: string description: Gene symbol, e.g., `"PCSK9"`. gene: type: string description: Gene ID, `e.g., "ENSG00000169174"`. feature_type: type: string description: Feature type, e.g., `"Transcript"`. feature: type: string description: Feature ID, e.g., `"ENST00000302118"`. feature_biotype: type: string description: Feature biotype, e.g., `"protein_coding"`. exon: type: - string - 'null' description: Ranked exon number, e.g., `"1/4"`. intron: type: - string - 'null' description: Ranked intron number, e.g., `"1/4"`. hgvsc: type: - string - 'null' description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`. hgvsp: type: - string - 'null' description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`. cdna_position: type: - string - 'null' description: cDNA position, e.g., `"89/1863"`. cds_position: type: - string - 'null' description: CDS position, e.g., `"89/1863"`. protein_position: type: - string - 'null' description: Protein position, e.g., `"30/620"`. amino_acids: type: - string - 'null' description: Amino acids, e.g., `"T/R"`. codons: type: - string - 'null' description: Codons, e.g., `"gCg/gGg"`. dbsnp_id: type: - string - 'null' description: |- TODO: actually is optional int32 allele_num = 18; dbSNP ID, e.g., `"rs28942080"`. distance: type: - string - 'null' description: Distance output of VEP. strand: type: - string - 'null' description: Strand, e.g., `"1"`. variant_class: type: - string - 'null' description: Variant class, e.g., `"SNV"`. minimised: type: - string - 'null' description: Minimised output of VEP. symbol_source: type: - string - 'null' description: Symbol source, e.g., `"HGNC"`. hgnc_id: type: - string - 'null' description: HGNC ID, e.g., `"HGNC:8706"`. canonical: type: - boolean - 'null' description: Whether this is the canonical transcript. tsl: type: - integer - 'null' format: int32 description: Transcript support level, e.g., `"1"`. appris: type: - string - 'null' description: APPRIS annotation, e.g. `"P1"`. ccds: type: - string - 'null' description: CCDS ID, e.g., `"CCDS30547.1"`. ensp: type: - string - 'null' description: Ensembl protein ID, e.g., `"ENSP00000302118"`. swissprot: type: - string - 'null' description: SwissProt ID, e.g., `"P04114"`. trembl: type: - string - 'null' description: TREMBL ID, e.g., `"Q5T4W7"`. uniparc: type: - string - 'null' description: UniParc ID, e.g., `"UPI000002D4B2"`. gene_pheno: type: - string - 'null' description: Gene phenotype from VEP. sift: oneOf: - type: 'null' - $ref: '#/components/schemas/VepCommonPrediction' description: SIFT prediction, e.g., `"tolerated(0.06)"`. polyphen: oneOf: - type: 'null' - $ref: '#/components/schemas/VepCommonPrediction' description: PolyPhen prediction, e.g., `"benign(0.001)"`. domains: type: array items: $ref: '#/components/schemas/VepCommonDomain' description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`. hgvs_offset: type: - string - 'null' description: HGVS offset. motif_name: type: - string - 'null' description: Motif name. motif_pos: type: - string - 'null' description: Motif name. high_inf_pos: type: - string - 'null' description: '"high inf pos" from VEP.' motif_score_change: type: - string - 'null' description: Motif score change. lof: type: - string - 'null' description: Loss of function prediction. lof_filter: type: - string - 'null' description: Loss of function filter. lof_flags: type: - string - 'null' description: Loss of function flags. lof_info: type: - string - 'null' description: Loss of function info. Gnomad4AncestryGroupAlleleCounts: type: object description: Store the allele counts for the given sub cohort in the given ancestry group. required: - ancestry_group properties: ancestry_group: type: string description: Name of the ancestry group. counts: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCountsBySex' description: The overall allele counts and the one by sex. faf95: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 95% CI). faf99: type: - number - 'null' format: float description: The filtering allele frequency (using Poisson 99% CI). faf95_xx: type: - number - 'null' format: float description: The filtering allele frequency for XX samples (using Poisson 95% CI). faf99_xx: type: - number - 'null' format: float description: The filtering allele frequency for XX samples (using Poisson 99% CI). faf95_xy: type: - number - 'null' format: float description: The filtering allele frequency for XY samples (using Poisson 95% CI). faf99_xy: type: - number - 'null' format: float description: The filtering allele frequency for XY samples (using Poisson 99% CI). Gnomad4CohortAlleleCounts: type: object description: Store the allele counts for the given cohort. required: - by_ancestry_group properties: cohort: type: - string - 'null' description: Name of the cohort. by_ancestry_group: type: array items: $ref: '#/components/schemas/Gnomad4AncestryGroupAlleleCounts' description: Allele counts for each population. by_sex: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCountsBySex' description: Allele counts by sex. raw: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AlleleCounts' description: Raw allele counts. grpmax: type: - string - 'null' description: The ancestry group with maximum AF. af_grpmax: type: - number - 'null' format: float description: Maximum allele frequency across ancestry groups. ac_grpmax: type: - integer - 'null' format: int32 description: Allele count in ancestry group with maximum AF. an_grpmax: type: - integer - 'null' format: int32 description: Total number of alleles in ancestry group with maximum AF. nhomalt_grpmax: type: - integer - 'null' format: int32 description: Total number of homozygous individuals in ancestry group with maximum AF. Gnomad4EffectInfo: type: object description: Store details on variant effect predictions. properties: pangolin_largest_ds: type: - number - 'null' format: float description: Pangolin's largest delta score across 2 splicing consequences, which reflects the probability of the variant being splice-altering"> phylop: type: - number - 'null' format: float description: Base-wise conservation score across the 241 placental mammals in the Zoonomia project. Score ranges from -20 to 9.28, and reflects acceleration (faster evolution than expected under neutral drift, assigned negative scores) as well as conservation (slower than expected evolution, assigned positive scores)."> polyphen_max: type: - number - 'null' format: float description: Score that predicts the possible impact of an amino acid substitution on the structure and function of a human protein, ranging from 0.0 (tolerated) to 1.0 (deleterious). We prioritize max scores for MANE Select transcripts where possible and otherwise report a score for the canonical transcript."> revel_max: type: - number - 'null' format: float description: The maximum REVEL score at a site's MANE Select or canonical transcript. It's an ensemble score for predicting the pathogenicity of missense variants (based on 13 other variant predictors). Scores ranges from 0 to 1. Variants with higher scores are predicted to be more likely to be deleterious."> sift_max: type: - number - 'null' format: float description: Score reflecting the scaled probability of the amino acid substitution being tolerated, ranging from 0 to 1. Scores below 0.05 are predicted to impact protein function. We prioritize max scores for MANE Select transcripts where possible and otherwise report a score for the canonical transcript."> spliceai_ds_max: type: - number - 'null' format: float description: Illumina's SpliceAI max delta score; interpreted as the probability of the variant being splice-altering."> cadd_raw: type: - number - 'null' format: float description: Raw CADD scores are interpretable as the extent to which the annotation profile for a given variant suggests that the variant is likely to be 'observed' (negative values) vs 'simulated' (positive values). Larger values are more deleterious. cadd_phred: type: - number - 'null' format: float description: Cadd Phred-like scores ('scaled C-scores') ranging from 1 to 99, based on the rank of each variant relative to all possible 8.6 billion substitutions in the human reference genome. Larger values are more deleterious. Gnomad4Record: type: object description: |- Protocol buffer for the gnomAD-nuclear VCF record. The more specialized fields from the INFO column are stored in separate, optional fields such that we don't end up with a humongous message. required: - chrom - pos - ref_allele - alt_allele - filters - vep - allele_counts - nonpar - only_het - outside_broad_capture_region - outside_ukb_capture_region - sibling_singleton properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: Alternate allele. filters: type: array items: $ref: '#/components/schemas/Gnomad3Filter' description: Site-level filters. vep: type: array items: $ref: '#/components/schemas/Gnomad4Vep' description: VEP annotation records. allele_counts: type: array items: $ref: '#/components/schemas/Gnomad4CohortAlleleCounts' description: |- Variant allele counts in the different cohorts and population. The populations in gnomAD v4 are: empty for global, "joint" for exome+genomes. nonpar: type: boolean description: Variant (on sex chromosome) falls outside a pseudoautosomal region only_het: type: boolean description: All samples are heterozygous for the variant outside_broad_capture_region: type: boolean description: Variant falls outside of Broad exome capture regions (exomes only). outside_ukb_capture_region: type: boolean description: Variant falls outside of UK Biobank exome capture regions(exomes only). sibling_singleton: type: boolean description: Variant was a callset-wide doubleton that was present only in two siblings (i.e., a singleton amongst unrelated samples in cohort) (exomes only). effect_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad4EffectInfo' description: Information on variant scores. variant_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3VariantInfo' description: Variant-related information details. quality_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3QualityInfo' description: Summary information for variant quality interpretation. age_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3AgeInfo' description: Age-related information. depth_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad3DepthInfo' description: Depth of coverage-related information. vrs_info: oneOf: - type: 'null' - $ref: '#/components/schemas/Gnomad4VrsInfo' description: VRS infos. Gnomad4Vep: type: object description: Protocol buffer for the gnomAD-nuclear VEP predictions. required: - allele - consequence - impact - symbol - gene - feature_type - feature - feature_biotype - domains properties: allele: type: string description: Allele of record. consequence: type: string description: Consequence, e.g., `"missense_variant"`. impact: type: string description: Impact, e.g., `"MODERATE"`. symbol: type: string description: Gene symbol, e.g., `"PCSK9"`. gene: type: string description: Gene ID, `e.g., "ENSG00000169174"`. feature_type: type: string description: Feature type, e.g., `"Transcript"`. feature: type: string description: Feature ID, e.g., `"ENST00000302118"`. feature_biotype: type: string description: Feature biotype, e.g., `"protein_coding"`. exon: type: - string - 'null' description: Ranked exon number, e.g., `"1/4"`. intron: type: - string - 'null' description: Ranked intron number, e.g., `"1/4"`. hgvsc: type: - string - 'null' description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`. hgvsp: type: - string - 'null' description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`. cdna_position: type: - string - 'null' description: cDNA position, e.g., `"89/1863"`. cds_position: type: - string - 'null' description: CDS position, e.g., `"89/1863"`. protein_position: type: - string - 'null' description: Protein position, e.g., `"30/620"`. amino_acids: type: - string - 'null' description: Amino acids, e.g., `"T/R"`. codons: type: - string - 'null' description: Codons, e.g., `"gCg/gGg"`. allele_num: type: - integer - 'null' format: int32 description: Allele count. distance: type: - string - 'null' description: Distance output of VEP. strand: type: - string - 'null' description: Strand, e.g., `"1"`. flags: type: - string - 'null' description: Flags variant_class: type: - string - 'null' description: Variant class, e.g., `"SNV"`. symbol_source: type: - string - 'null' description: Symbol source, e.g., `"HGNC"`. hgnc_id: type: - string - 'null' description: HGNC ID, e.g., `"HGNC:8706"`. canonical: type: - boolean - 'null' description: Whether this is the canonical transcript. mane_select: type: - boolean - 'null' description: Presence in MANE Select mane_plus_clinical: type: - boolean - 'null' description: Presence in MANE Plus Clinical tsl: type: - integer - 'null' format: int32 description: Transcript support level, e.g., `"1"`. appris: type: - string - 'null' description: APPRIS annotation, e.g. `"P1"`. ccds: type: - string - 'null' description: CCDS ID, e.g., `"CCDS30547.1"`. ensp: type: - string - 'null' description: Ensembl protein ID, e.g., `"ENSP00000302118"`. uniprot_isoform: type: - string - 'null' description: Uniprot isoform. source: type: - string - 'null' description: Value of VEP "SOURCE" field. domains: type: array items: $ref: '#/components/schemas/VepCommonDomain' description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`. mirna: type: - string - 'null' description: miRNA information. hgvs_offset: type: - string - 'null' description: HGVS offset. pubmed: type: - string - 'null' description: PubMed IDs motif_name: type: - string - 'null' description: Motif name. motif_pos: type: - string - 'null' description: Motif name. high_inf_pos: type: - string - 'null' description: '"high inf pos" from VEP.' motif_score_change: type: - string - 'null' description: Motif score change. transcription_factors: type: - string - 'null' description: Transcription factors. lof: type: - string - 'null' description: Loss of function prediction. lof_filter: type: - string - 'null' description: Loss of function filter. lof_flags: type: - string - 'null' description: Loss of function flags. lof_info: type: - string - 'null' description: Loss of function info. Gnomad4VrsInfo: type: object description: VRS information required: - allele_ids - ends - starts - states properties: allele_ids: type: array items: type: string description: The computed identifiers for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields ends: type: array items: type: integer format: int32 description: Interresidue coordinates used as the location ends for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields starts: type: array items: type: integer format: int32 description: Interresidue coordinates used as the location starts for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields states: type: array items: type: string description: The literal sequence states used for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields GnomadMtdnaAgeInfo: type: object description: Encapsulate VCF INFO fields related to age. required: - age_hist_hom_bin_freq - age_hist_het_bin_freq properties: age_hist_hom_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]. age_hist_hom_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a homoplasmic variant. age_hist_hom_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a homoplasmic variant. age_hist_het_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0, 40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0] age_hist_het_n_smaller: type: - integer - 'null' format: int32 description: |- Count of age values falling below lowest histogram bin edge for individuals with a heteroplasmic variant. age_hist_het_n_larger: type: - integer - 'null' format: int32 description: |- Count of age values falling above highest histogram bin edge for individuals with a heteroplasmic variant. GnomadMtdnaDepthInfo: type: object description: Encapsulate VCF INFO fields related to depth. required: - dp_hist_all_bin_freq - dp_hist_alt_bin_freq properties: dp_hist_all_n_larger: type: - integer - 'null' format: int32 description: Count of dp values falling above highest histogram bin edge for all individuals. dp_hist_alt_n_larger: type: - integer - 'null' format: int32 description: |- Count of dp values falling above highest histogram bin edge for individuals with the alternative allele dp_hist_all_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] dp_hist_alt_bin_freq: type: array items: type: integer format: int32 description: |- Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0] GnomadMtdnaFilter: type: string description: Protocol buffer enum for site-level filters. enum: - artifact_prone_site - indel_stack - no_pass_genotype GnomadMtdnaFilterHistograms: type: object description: Encapsulate VCF INFO fields related to filter failure histograms. required: - base_qual_hist - position_hist - strand_bias_hist - weak_evidence_hist - contamination_hist properties: base_qual_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals failing the base_qual filter (alternate allele median base quality) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] position_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals failing the position filter (median distance of alternate variants from end of reads) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0. 30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] strand_bias_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals failing the strand_bias filter (evidence for alternate allele comes from one read direction only) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] weak_evidence_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals failing the weak_evidence filter (mutation does not meet likelihood threshold) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] contamination_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals failing the contamination filter across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] GnomadMtdnaHaplogroupInfo: type: object description: Encapsulate VCF INFO fields related to haplogroups. required: - hap_defining_variant - hap_an - hap_ac_het - hap_ac_hom - hap_af_het - hap_af_hom - hap_hl_hist - hap_faf_hom properties: hap_defining_variant: type: boolean description: Present if variant is present as a haplogroup defining variant in PhyloTree build 17. hap_an: type: array items: type: integer format: int32 description: |- List of overall allele number for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hap_ac_het: type: array items: type: integer format: int32 description: |- List of AC_het for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hap_ac_hom: type: array items: type: integer format: int32 description: |- List of AC_hom for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hap_af_het: type: array items: type: number format: float description: |- List of AF_het for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hap_af_hom: type: array items: type: number format: float description: |- List of AF_hom for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hap_hl_hist: type: array items: type: integer format: int32 description: |- Histogram of heteroplasmy levels for each haplogroup; bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0], haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] Note that we encode this by concatenating all lists here because of limitations in protocolbuffers (no native nested repeated fields). hap_faf_hom: type: array items: type: number format: float description: |- List of filtering allele frequency for each haplogroup restricted to homoplasmic variants, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] hapmax_af_hom: type: - string - 'null' description: Haplogroup with maximum AF_hom. hapmax_af_het: type: - string - 'null' description: Haplogroup with maximum AF_het. faf_hapmax_hom: type: - number - 'null' format: float description: Maximum filtering allele frequency across haplogroups restricted to homoplasmic variants. GnomadMtdnaHeteroplasmyInfo: type: object description: Encapsulate VCF INFO fields related to heteroplasmy levels. required: - heteroplasmy_below_min_het_threshold_hist - hl_hist - common_low_heteroplasmy - max_hl properties: heteroplasmy_below_min_het_threshold_hist: type: array items: type: integer format: int32 description: |- Histogram of number of individuals with a heteroplasmy level below 0.1, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0] hl_hist: type: array items: type: integer format: int32 description: |- Histogram of heteroplasmy levels; bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0]. common_low_heteroplasmy: type: boolean description: |- Present if variant is found at an overall frequency of .001 across all samples with a heteroplasmy level > 0 and < 0.50 (includes variants <0.01 heteroplasmy which are subsequently filtered) max_hl: type: number format: float description: Maximum heteroplasmy level observed among all samples for that variant. GnomadMtdnaPopulationInfo: type: object description: Encapsulate VCF INFO fields related to populations. required: - pop_an - pop_ac_het - pop_ac_hom - pop_af_hom - pop_af_het - pop_hl_hist properties: pop_an: type: array items: type: integer format: int32 description: |- List of overall allele number for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'] pop_ac_het: type: array items: type: integer format: int32 description: |- List of AC_het for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'] pop_ac_hom: type: array items: type: integer format: int32 description: |- List of AC_hom for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'] pop_af_hom: type: array items: type: number format: float description: |- List of AF_hom for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'] pop_af_het: type: array items: type: number format: float description: |- List of AF_het for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'] pop_hl_hist: type: array items: type: integer format: int32 description: |- Histogram of heteroplasmy levels for each population; bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0], population order: \['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'\] Note that we encode this by concatenating all lists here because of limitations in protocolbuffers (no native nested repeated fields). GnomadMtdnaQualityInfo: type: object description: Encapsulate VCF INFO fields related to quality. properties: dp_mean: type: - number - 'null' format: float description: Mean depth across all individuals for the site. mq_mean: type: - number - 'null' format: float description: Mean MMQ (median mapping quality) across individuals with a variant for the site. tlod_mean: type: - number - 'null' format: float description: |- Mean TLOD (Log 10 likelihood ratio score of variant existing versus not existing) across individuals with a variant for the site. GnomadMtdnaRecord: type: object description: |- Protocol buffer for the gnomAD-mtDNA VCF record. The more specialized fields from the INFO column are stored in separate, optional fields such that we don't end up with a humongous message. required: - chrom - pos - ref_allele - alt_allele - variant_collapsed - excluded_ac - an - ac_hom - ac_het - af_hom - af_het - filters - vep properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: Alternate allele. variant_collapsed: type: string description: Variant in format of RefPosAlt excluded_ac: type: integer format: int32 description: Excluded allele count (number of individuals in which the variant was filtered out). an: type: integer format: int32 description: Overall allele number (number of samples with non-missing genotype). ac_hom: type: integer format: int32 description: Allele count restricted to variants with a heteroplasmy level >= 0.95. ac_het: type: integer format: int32 description: Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95. af_hom: type: number format: float description: Allele frequency restricted to variants with a heteroplasmy level >= 0.95. af_het: type: number format: float description: Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95. filters: type: array items: $ref: '#/components/schemas/GnomadMtdnaFilter' description: Site-level filters. mitotip_score: type: - number - 'null' format: float description: MitoTip raw score mitotip_trna_prediction: type: - string - 'null' description: MitoTip score interpretation pon_mt_trna_prediction: type: - string - 'null' description: tRNA pathogenicity classification from PON-mt-tRNA pon_ml_probability_of_pathogenicity: type: - string - 'null' description: tRNA ML_probability_of_pathogenicity from PON-mt-tRNA vep: type: array items: $ref: '#/components/schemas/Gnomad3Vep' description: VEP v3 annotation records. quality_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaQualityInfo' description: Summary information for variant quality interpretation. heteroplasmy_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaHeteroplasmyInfo' description: Information related to heteroplasmy levels. filter_histograms: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaFilterHistograms' description: Histograms related to variant quality filters. population_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaPopulationInfo' description: Population-related information. haplogroup_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaHaplogroupInfo' description: Haplogroup-related information. age_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaAgeInfo' description: Age-related information. depth_info: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaDepthInfo' description: Depth of coverage-related information. GnomadRecord: oneOf: - type: object description: gnomAD v2 record. required: - gnomad2 properties: gnomad2: $ref: '#/components/schemas/Gnomad2Record' description: gnomAD v2 record. - type: object description: gnomAD v3 record. required: - gnomad3 properties: gnomad3: $ref: '#/components/schemas/Gnomad3Record' description: gnomAD v3 record. - type: object description: gnomAD v4 record. required: - gnomad4 properties: gnomad4: $ref: '#/components/schemas/Gnomad4Record' description: gnomAD v4 record. description: Allow either a gnomAD v2/v3 or v4 record. HelixMtDbRecord: type: object description: A HelixMtDb record. required: - chrom - pos - ref_allele - alt_allele - num_total - num_het - num_hom - feature_type - gene_name properties: chrom: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based start position. ref_allele: type: string description: Reference allele. alt_allele: type: string description: / Alternate allele. num_total: type: integer format: int32 description: Total number of individuals. num_het: type: integer format: int32 description: Number of homoplasmic carriers. num_hom: type: integer format: int32 description: Number of heteroplasmic carriers. feature_type: type: string description: Feature type. gene_name: type: string description: Gene name. Scored: type: object description: A scored result. required: - score - data properties: score: type: number format: float description: The score. data: $ref: '#/components/schemas/GeneNames' description: The result. SeqvarsAnnoResponseRecord: type: object description: Annotation for a sinngle variant. properties: cadd: type: - object - 'null' description: Annotations from CADD (TSV annotation file). additionalProperties: {} propertyNames: type: string dbsnp: oneOf: - type: 'null' - $ref: '#/components/schemas/DbsnpRecord' description: Annotations from dbSNP. dbnsfp: type: - object - 'null' description: Annotations from dbNSFP (TSV annotation file). additionalProperties: {} propertyNames: type: string dbscsnv: type: - object - 'null' description: Annotations from dbscSNV. additionalProperties: {} propertyNames: type: string gnomad_mtdna: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadMtdnaRecord' description: Annotations from gnomAD-mtDNA. gnomad_exomes: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadRecord' description: Annotations from gnomAD-exomes. gnomad_genomes: oneOf: - type: 'null' - $ref: '#/components/schemas/GnomadRecord' description: Annotations from gnomAD-genomes. helixmtdb: oneOf: - type: 'null' - $ref: '#/components/schemas/HelixMtDbRecord' description: Annotations from HelixMTdb. ucsc_conservation: oneOf: - type: 'null' - $ref: '#/components/schemas/UcscConservationRecordList' description: Annotations from UCSC conservation. clinvar: oneOf: - type: 'null' - $ref: '#/components/schemas/ExtractedVcvRecordList' description: Minimal extracted data from ClinVar. SeqvarsAnnosQuery: type: object description: |- Parameters for `variant_annos::handle`. Defines a variant in VCF-style format with a genome release specification. required: - genome_release - chromosome - pos - reference - alternative properties: genome_release: type: string description: Genome release specification. chromosome: type: string description: Chromosome name. pos: type: integer format: int32 description: 1-based position for VCF-style variant. minimum: 0 reference: type: string description: Reference allele bases. alternative: type: string description: Alterantive allele bases. SeqvarsAnnosResponse: type: object description: Query response for `handle_with_openapi()`. required: - result properties: result: $ref: '#/components/schemas/SeqvarsAnnoResponseRecord' description: The result records. StrucvarsClinvarPageInfo: type: object description: Information regarding the pagination. required: - total - per_page - current_page - total_pages properties: total: type: integer format: int32 description: The total number of records. minimum: 0 per_page: type: integer format: int32 description: The number of records per page. minimum: 0 current_page: type: integer format: int32 description: The current page number. minimum: 0 total_pages: type: integer format: int32 description: The total number of pages. minimum: 0 StrucvarsClinvarQuery: type: object description: Query of the `/api/v1/strucvars/clinvar-annos/query` endpoint. required: - genome_release - chromosome - start - stop properties: genome_release: $ref: '#/components/schemas/GenomeRelease' description: Genome release specification. chromosome: type: string description: Chromosome name. start: type: integer format: int32 description: 1-based start position. minimum: 0 stop: type: integer format: int32 description: 1-based stop postion. minimum: 0 variation_types: type: - array - 'null' items: $ref: '#/components/schemas/ClinvarExtractedVariationType' description: Optionally, the variant types. min_overlap: type: - number - 'null' format: double description: Optionally, minimal overlap. page_no: type: - integer - 'null' format: int32 description: Optional 1-based page number. minimum: 0 page_size: type: - integer - 'null' format: int32 description: Optional page size. minimum: 0 StrucvarsClinvarResponse: type: object description: Response of the `/api/v1/strucvars/clinvar-annos/query` endpoint. required: - records - page_info properties: records: type: array items: $ref: '#/components/schemas/StrucvarsClinvarResponseRecord' description: The records in this page. page_info: $ref: '#/components/schemas/StrucvarsClinvarPageInfo' description: Pagination information. StrucvarsClinvarResponseRecord: type: object description: Information on one response record. required: - overlap properties: record: oneOf: - type: 'null' - $ref: '#/components/schemas/ClinvarExtractedVcvRecord' description: The record. overlap: type: number format: double description: The reciprocal overlap with the query. UcscConservationRecord: type: object description: A UCSC conservation record. required: - chrom - start - stop - hgnc_id - enst_id - exon_num - exon_count - alignment properties: chrom: type: string description: Chromosome name. start: type: integer format: int32 description: 1-based, inclusive start position. stop: type: integer format: int32 description: 1-based, inclusive stop position. hgnc_id: type: string description: HGNC identifier. enst_id: type: string description: ENST identifier. exon_num: type: integer format: int32 description: Exon number (1-based). exon_count: type: integer format: int32 description: Exon count. alignment: type: string description: Alignment. UcscConservationRecordList: type: object description: List of `Record`s. required: - records properties: records: type: array items: $ref: '#/components/schemas/UcscConservationRecord' description: The records in the list. VepCommonDomain: type: object description: Protocol buffer for `Vep.domains` required: - id - source properties: id: type: string description: Domain ID. source: type: string description: Domain source. VepCommonPrediction: type: object description: Store the scoring of a prediction. required: - prediction - score properties: prediction: type: string description: Prediction. score: type: number format: float description: Score. VersionsAnnotationInfo: type: object description: Version information for one database. required: - database properties: database: $ref: '#/components/schemas/AnnoDb' description: Database name. version_spec: oneOf: - type: 'null' - $ref: '#/components/schemas/VersionsVersionSpec' description: Version information of the database. VersionsCreatedFrom: type: object description: Source name and version. required: - name - version properties: name: type: string description: The name of the data source. version: type: string description: The version of the data source. VersionsInfoQuery: type: object description: Query parameters for `handle()`. VersionsInfoResponse: type: object description: Response for `handle()`. properties: genes: oneOf: - type: 'null' - $ref: '#/components/schemas/VersionsVersionSpec' description: Version information of the genes. seqvars: type: array items: $ref: '#/components/schemas/VersionsPerRelease' description: Version information of annotation databases per release. VersionsPerRelease: type: object description: Version information for databases in a given release. required: - release properties: release: $ref: '#/components/schemas/GenomeRelease' description: The genome release. version_infos: type: array items: $ref: '#/components/schemas/VersionsAnnotationInfo' description: Version information of annotation databases. VersionsVersionSpec: type: object description: Version specification. required: - identifier - title - creator - contributor - format - date - version - description - source - created_from properties: identifier: type: string description: Identifier of the data. title: type: string description: Title of the data. creator: type: string description: Creator of the data. contributor: type: array items: type: string description: Contributors of the data. format: type: string description: Format of the data. date: type: string description: Date of the data. version: type: string description: Version of the data. genome_release: type: - string - 'null' description: Optional genome release. description: type: string description: Data description. source: type: array items: type: string description: Data source. created_from: type: array items: $ref: '#/components/schemas/VersionsCreatedFrom' description: Created from information.