Exomiser Interpretation Service Data

Exomiser Service v1.1.4

*Mandatory field

The Exomiser v1.1.4 service produces an Interpreted Genome with the following fields populated

Data DescriptionExample Response

Field Name	Type	Description
comments	array[string];	Always null
variants	array[SmallVariant];	List of small reported variants by Exomiser service. An empty list will indicate the absence of reported small variants for this case.
reportUrl	string	Fixed value. Always empty string, exomiser service does not expose or serves its results
karyotypes	array[Karyotype];	Always null. Exomiser service does not perform analysis for Karyotypes
versionControl*	ReportVersionControl	Exomiser data is represented using version 6.0.0 of Interpreted Genome Model. More details: https://gelreportmodels.genomicsengland.co.uk/html_schemas/org.gel.models.report.avro/6.0.0/InterpretedGenome.html#/schema/org.gel.models.report.avro.InterpretedGenome
softwareVersions*	map[string, string];	This map contains the versions of the different software systems used in the analysis, the keys being the software names and the versions are the values.
shortTandemRepeats		Always null. Exomiser service does not perform analysis for Short Tandem Repeats
structuralVariants	array[StructuralVariant];	Always null. Exomiser service does not perform analysis for structural variants
uniparentalDisomies	array[UniparentalDisomy];	Always null. Exomiser service does not perform analysis for uniparentalDisomies
interpretationService*	string	Fixed value. Exomiser
interpretationRequestId*	string	Full id of the case in the cipapi. Generally something like: SAP-XXXX-XX
chromosomalRearrangements	array[ChromosomalRearrangement]	Always null. Exomiser service does not perform analysis for chromosomal Rearrangements
referenceDatabasesVersions*	map[string, string];	This map contains the versions of the different databases used in the analysis, being the database names the keys and the versions the values.
interpretationRequestVersion	integer	Version for the interpretation request. This will be the case version in the cipapi

    interpreted_genome_data: {
    comments: null,
    variants: [],
    reportUrl: "",
    karyotypes: null,
    versionControl: {},
    softwareVersions: {},
    shortTandemRepeats: null,
    structuralVariants: null,
    uniparentalDisomies: null,
    interpretationService: "Exomiser",
    interpretationRequestId: "SAP-3106-1",
    chromosomalRearrangements: null,
    referenceDatabasesVersions: {},
    interpretationRequestVersion: 1
    },

Exomiser Service V1.1.4 - SmallVariant

Data DescriptionExample Response

Field Name	Type	Description
reportEvents*	array[ReportEvent]	The list of report events for this variant across multiple modes of inheritance, panels and
variantCalls*	array[VariantCall]	List of variant calls across all samples under analysis for this variant
variantAttributes	VariantAttributes	A set of variant attributes
variantCoordinates*	VariantCoordinates	The variant coordinates. Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome. No chr prefix is expected. Position is 1- based. Reference and alternate should never be empty or any character representing emptiness (e.g.: . or -). A VCF-like indel representation is expected.

    {
    reportEvents: [...],
    variantCalls: [...],
    variantAttributes: {...},
    variantCoordinates: {...}
    },

Exomiser Service V1.1.4 - VariantCoordinates

Data DescriptionExample Response

Field Name	Type	Description
assembly	string	Fixed Value. GRCh38
position	integer	Position is 1- based
alternate	string	Alternate should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
reference	string	Reference should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
chromosome	string	Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected

    variantCoordinates: {
    assembly: "GRCh38",
    position: 94380925,
    alternate: "A",
    reference: "T",
    chromosome: "14"
    }

Exomiser Service V1.1.4 - ReportEvents

Data DescriptionExample Response

Field Name	Type	Description
tier	Tier	Always null. Exomiser does not use tier to classify variants
score	float	Exomiser will populate here the final score for the report event which is calculated by a logistic regression model is used to combine the phenotype and variant scores.
domain	Domain	Always null. Exomiser does not use domain to classify variants
actions	Actions	Always null. Exomiser does not use actions to classify variants
genePanel	GenePanel	Always null. Exomiser does not use GenePanels in its analysis
penetrance	Penetrance (enumeration)	This is the penetrance assumed for scoring or classifying this variant
phenotypes*	Phenotypes	List of phenotypes relevant to this report event
roleInCancer	array[RoleInCancer]	Always null. Exomiser does not use roleInCancer to classify variants
reportEventId*	Integer	Unique identifier for each report event, this is unique across the whole report.
genomicEntities	array[GenomicEntity]	List of all of the genomic entities relevant for this report event. This version of exomiser does not report on transcripts but only at the gene level, therefore is expected to find a single gene entry in this list.
groupOfVariants	integer	This value groups variants that together could explain the phenotype according to the mode of inheritance used. (e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in the same group (i.e.: reported together). This value is an integer unique in the whole report. These values are only relevant within the same report.
modeOfInheritance*	ModeOfInheritance (enumeration)	Mode of inheritance reported for this report event
deNovoQualityScore	float	Always null. Exomiser does not use deNovoQualityScore to classify variants
eventJustification	string	This is the description of why this variant would be reported. Exomiser add the values and IDs of the phenotypes and the protein from model organisms taken in account in this report event
segregationPattern	SegregationPattern (enumeration)	Always null. Exomiser does not populate this field
variantConsequences*	array[VariantConsequence]	Always an empty list, exomiser does not populate the list of consequences. Exomiser stores the consequence type in the additionalNumericVariantAnnotations.
vendorSpecificScores	map[string, float]	Exomiser uses this field to populate the values used for the variant classification. There scores reported include: 1. genePhenoScore : score for this gene (on a scale of 0 to 1) based on how phenotypically similar the patient's phenotypes are to (i) OMIM and Orphanet rare diseases known to be associated with the gene, (ii) mouse and zebrafish models associated with the orthologue of the gene, and (iii) disease, mouse or zebrafish phenotypes associated with neighbouring genes in the StringDB protein-protein association database (scores weighted down based on network distance from the gene under consideration). 2.geneVariantScore : For each MOI, the highest scoring compatible variant for each gene, or top two highest for compound-heterozygous candidates, are then selected as the contributing variant(s) for that gene under that MOI and used to assign a gene-level variant score (taking the mean for compound heterozygotes. 3. rank : The maximum Exomiser score out of any of the reportEvents for a variant is used to rank all of the returned variants with rank = 1 representing the most-likely candidate according to Exomiser and hopefully describing a rare, predicted pathogenic variant that disrupts a gene that has previously been associated with similar phenotypes to the patient. 4. variantScore:score for how rare and pathogenic each variant is (on a scale of 0 to 1) using the above frequency sources and predicted pathogenicity scores by Revel and MVP
variantClassification	VariantClassification	Always null. Exomiser does not use variantClassification to classify variants
fullyExplainsPhenotype	boolean	Always null. Exomiser does not populate this field
guidelineBasedVariantClassification	GuidelineBasedVariantClassification	Always null. Exomiser does not use guidelineBasedVariantClassification to classify variants
algorithmBasedVariantClassifications	array[AlgorithmBasedVariantClassification]	Always null. Exomiser does not use algorithmBasedVariantClassifications to classify variants

    {
    tier: null,
    score: 0.7556089,
    domain: null,
    actions: null,
    genePanel: null,
    penetrance: "complete",
    phenotypes: {},
    roleInCancer: null,
    reportEventId: "1",
    genomicEntities: [],
    groupOfVariants: 1,
    modeOfInheritance: "biallelic",
    deNovoQualityScore: null,
    eventJustification: "MOUSE_PPI=MGI:1924301_24168,Progressive cervical vertebral spine fusion (HP:0008449)-vertebral fusion (MP:0004609),Partial fusion of tarsals (HP:0008097)-vertebral fusion (MP:0004609),Partial fusion of carpals (HP:0006207)-vertebral fusion (MP:0004609),Posterior fusion of lumbosacral vertebrae (HP:0005626)-vertebral fusion (MP:0004609),Back pain (HP:0003418)-vertebral fusion (MP:0004609),Irregular vertebral endplates (HP:0003301)-vertebral fusion (MP:0004609),Kyphosis (HP:0002808)-vertebral fusion (MP:0004609),Abnormality of the vertebral column (HP:0000925)-vertebral fusion (MP:0004609)",
    segregationPattern: null,
    variantConsequences: [ ],
    vendorSpecificScores: {},
    variantClassification: {},
    fullyExplainsPhenotype: null,
    guidelineBasedVariantClassification: null,
    algorithmBasedVariantClassifications: null
    }

Exomiser Service V1.1.4 - GenomicEntities

Data DescriptionExample Response

Field Name	Type	Description
type*	GenomicEntityType (enumeration)	The type of the genomic entity. gene is the only value expected for Exomiser in this field.
otherIds	array[Identifier]	Always null. Exomiser does not use any other identifiers.
ensemblId	string	Ensembl identifier for the feature.
geneSymbol	string	The HGNC gene symbol. Exomiser will always populate this field with the gene symbol.

    genomicEntities: [
    {
    type: "gene",
    otherIds: null,
    ensemblId: "ENSG00000084110",
    geneSymbol: "HAL"
    }
    ],

Exomiser Service V1.1.4 - VariantCalls

Data DescriptionExample Response

Field Name	Type	Description
sampleId*	string	Sample id
zygosity*	Zygosity(enumeration)	Variant zygosity
alleleOrigins	array[AlleleOrigin];	Fixed value: ["germline_variant"]. Exomiser analysis is only for germline variants
participantId*	string	Participant id
phaseGenotype	PhaseGenotype	Always null. Exomiser does not populate this field
depthAlternate	integer	Always null. Exomiser does not populate this field
depthReference	integer	Always null. Exomiser does not populate this field
numberOfCopies	array[NumberOfCopies]	Always null. Exomiser does not populate this field
supportingReadTypes	SupportingReadType(enumeration)	Always null. Exomiser does not populate this field
sampleVariantAlleleFrequency	double	Always null. Exomiser does not populate this field

{
variantCalls: [
{
sampleId: "LP3001324-DNA_D12",
zygosity: "heterozygous",
alleleOrigins: ["germline_variant"],
participantId: "p72748341269",
phaseGenotype: null,
depthAlternate: null,
depthReference: null,
numberOfCopies: null,
supportingReadTypes: null,
sampleVariantAlleleFrequency: null
},
},
]

Exomiser Service V1.1.4 - VariantAttributes

Data DescriptionExample Response

Field Name	Type	Description
ihp	integer	Always null. Exomiser does not populate this field
fdp50	float	Always null. Exomiser does not populate this field
others	map[string]	Always null. Exomiser does not populate this field
comments	array[string]	Always null. Exomiser does not populate this field
references	map[string]	Always null. Exomiser does not populate this field
cdnaChanges	array[string]	Always null. Exomiser does not populate this field
alleleOrigins	array[AlleleOrigin]	Fixed value: germline_variant. Exomiser analysis is only for germline variants
genomicChanges	array[string]	Always null. Exomiser does not populate this field
proteinChanges	array[string]	Always null. Exomiser does not populate this field
alleleFrequencies	array[AlleleFrequency]	Always null. Exomiser does not populate this field
variantIdentifiers	VariantIdentifiers	Exomiser does not populate values for variant identifiers. A fixed value with all inner fields are expected to be null: { "cosmicIds": null, "clinVarIds": null, "otherIds": null, "dbSnpId": null }
recurrentlyReported	boolean	Always null. Exomiser does not populate this field
additionalTextualVariantAnnotations	map[string]	Any additional information in a free text field. Exomiser uses this field to report the consequence type and the HGVS nomenclature of the variant for a chosen transcript. The keys of the expected values in the dictionary are maxFrequency for the overall maximum allele (population) frequency including external and internal populations and gelFrequency for the maximum internal allele frequency
additionalNumericVariantAnnotations	map[float]	Exomiser uses this field to report the highest allele frequencies internal and external, it also reports on the highest internal allele frequency found. . The keys of the expected values in the dictionary are consequence for the variant consequence type (most damaging one), and hgvs for the HGVS nomenclature of the variant

{
variantAttributes: {
    ihp: null,
    fdp50: null,
    others: null,
    comments: null,
    references: null,
    cdnaChanges: null,
    alleleOrigins: [],
    genomicChanges: null,
    proteinChanges: null,
    alleleFrequencies: null,
    variantIdentifiers: {
        dbSnpId: null,
        otherIds: null,
        cosmicIds: null,
        clinVarIds: null
        },
    recurrentlyReported: null,
    additionalNumericVariantAnnotations: {
        gelFrequency: 0.407424,
        maxFrequency: 0.5819
        },
    additionalTextualVariantAnnotations: {
        hgvs: "HAL:ENST00000261208.7:c.1106G>A:p.(Arg369Gln)",
        consequence: "missense_variant"
        }
    },
}

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Last update: 2022-03-25