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
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¶
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. |
Exomiser Service V1.1.4 - VariantCoordinates¶
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 |
Exomiser Service V1.1.4 - ReportEvents¶
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¶
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. |
Exomiser Service V1.1.4 - VariantCalls¶
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¶
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"
}
},
}
Last update:
2022-03-25