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Interpretation Portal Clinical Report Data

Description of the Clinical Report Data produced from Interpretation Portal (Interpretation Portal v2.7.0-b4. Interpretation API 2.9.1b1)

IP RD ClinicalReport

Field Name Type Description
interpretationRequestId* string This is the interpretation request identifier (i.e. the 123 in SAP-123-1)
interpretationRequestVersion int This is the version of the interpretation request identifier (i.e. the 1 in SAP-123-1)
reportingDate string Date of this report in format YYYY-MM-DD
user string Author of this report, this will be the Azure Active Directory user ID
variants array[SmallVariant] List of small variants that have been flagged by users as Primary Findings in the Interpretation Portal
structuralVariants array[StructuralVariant] List of simple structural variants (duplications, deletions, insertions, inversions, CNVs) that have been flagged by users as Primary Findings in the Interpretation Portal
chromosomalRearrangements array[ChromosomalRearrangement] Always null. Interpretation Platform currently does not perform analysis for Chromosomal Rearrangements
shortTandemRepeats array[ShortTandemRepeat] List of STRs that have been flagged by users as Primary Findings in the Interpretation Portal
uniparentalDisomies array[UniparentalDisomy] Always null. UPDs are not reported in Interpretation Portal
karyotypes array[Karyotype] Always null. Karyotypes are not reported in Interpretation Portal
genomicInterpretation string Free text comments added into the clinical report
additionalAnalysisPanels array[AdditionalAnalysisPanel] Always null
references array[string] Array of free text fields for users to enter PubMed IDs for literature references
referenceDatabasesVersions map[string] For Interpretation Portal clinical reports, this field will contain the reference genome assembly used for this case.
softwareVersions map[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. 
clinicalReportData": {
"interpretationRequestId": "123",
"interpretationRequestVersion": 1,
"reportingDate": "2001-01-01",
"user": "999999-a9a9-99a0-a99a-a9aaa9aaaa9a",
"variants": [...],
"structuralVariants": [...],
"chromosomalRearrangements": null,
"shortTandemRepeats": [...],
"genomicInterpretation": "example of a case level interpretative comment made for a clinical report in the Interpretation Portal",
"additionalAnalysisPanels": null,
"references": ["12345678"],
"referenceDatabasesVersions": {"genomeAssembly": "GRCh38"},
"softwareVersions": {
  "vt": "ee9a751",
  "bcftools": "v1.2",
  "cellbase": "v4.7.1",
  "platypus": "v0.8.1",
  "gel-tiering": "1.4.0",
  "gel-coverage": "1.4.3",
  "gitVersionControl": "6.0.2"
}

IP RD ClinicalReport - SmallVariant

Field Name Type Description
variantCoordinates* VariantCoordinates The variant coordinates.
variantCalls* array[VariantCall] List of variant calls across all samples under analysis for this variant
reportEvents* array[ReportEvent] The list of report events for this variant across multiple modes of inheritance and panels
variantAttributes VariantAttributes Variant attributes 
"variants": [
  {
    "variantCoordinates": {...},
    "variantCalls": [...],
    "reportEvents": [...],
    "variantAttributes": {...}
  },
]

IP RD ClinicalReport - StructuralVariant

Field Name Type Description
variantType StructuralVariantType (enumeration) One of ins, dup, inv, amplification, deletion, dup_tandem, del_me, ins_me
coordinates Coordinates The variant coordinates.
leftInsSeq string Always null. rare disease tiering does not populate this field
rightInsSeq string Always null. rare disease tiering does not populate this field
reportEvents array[ReportEvent] The list of report events for this variant across multiple modes of inheritance and panels
variantCalls array[VariantCall] List of variant calls across all samples under analysis for this variant
variantAttributes VariantAttributes Variant attributes 
"structuralVariants": [
  {
    "variantType": "amplification",
    "coordinates": {...},
    "leftInsSeq": null,
    "rightInsSeq": null,
    "reportEvents": [...],
    "variantCalls": [...],
    "variantAttributes": {...}
  }
],

IP RD ClinicalReport - ShortTandemRepeat

Field Name Type Description
coordinates Coordinates The variant coordinates.
reportEvents array[ReportEvent] The list of report events for this variant across multiple modes of inheritance and panels
variantCalls array[VariantCall] List of variant calls across all samples under analysis for this variant
variantAttributes VariantAttributes Variant attributes
shortTandemRepeatReferenceData ShortTandemRepeatReferenceData Contains the repeated sequence, pathogenic number of repeats threshold and normal number of repeats threshold

IP RD ClinicalReport - STR Coordinates

Unlike Small variants, which use the Va riantCoordinates model, CNVs, SVs, STRs use the "Coordinates" data model

Field Name Type Description
assembly string GRCh37 or GRCh38
chromosome string Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected
start integer Position is 1- based
end integer Position is 1- based
ciStart null ConfidenceInterval
ciEnd null ConfidenceInterval 
"coordinates": {
  "assembly": "GRCh38",
  "chromosome": "6",
  "start": 73747596,
  "end": 73765265,
  "ciStart": null,
  "ciEnd": null
}

IP RD ClinicalReport - VariantCoordinates

Field Name Type Description
assembly string GRCh37 or GRCh38
chromosome string Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected
position integer Position is 1- based
reference string Reference should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
alternate string Alternate should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected 
"variantCoordinates": {
  "chromosome": "1",
  "position": 9999999999,
  "reference": "A",
  "alternate": "G",
  "assembly": "GRCh38"
}

IP RD ClinicalReport - ReportEvent

Field Name Type Description
reportEventId* Integer Unique identifier for each report event, this is unique across the whole report.
phenotypes* Phenotypes List of phenotypes relevant to this report event
variantConsequences* array[VariantConsequence] List of consequence types and their SO IDs for the report event
genePanel GenePanel The panel of genes to which this report corresponds
modeOfInheritance* ModeOfInheritance (enumeration) Mode of inheritance reported for this report event
genomicEntities array[GenomicEntity] List of all of the genomic entities relevant for this report event.
segregationPattern SegregationPattern (enumeration) This is the segregation pattern used for scoring or classifying this variant
penetrance Penetrance (enumeration) This is the penetrance assumed for scoring or classifying this variant
deNovoQualityScore float Likelihood of being a de novo variant. Only present if thge varaiant has been previously flagged as de novo by tiering
fullyExplainsPhenotype boolean Always null. Interpretation Portal does not populate this field
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.
eventJustification string Always null. Interpretation Portal does not populate this field.
roleInCancer array[RoleInCancer] Always null. This field does not apply to Rare Disease cases.
actions Actions Always null. Interpretation Portal does not use actions to classify variants
score float Always null. Interpretation Portal does not populate this field.
vendorSpecificScores map[string, float] Always null. Interpretation Portal does not use vendorSpecificScores to classify variants
variantClassification VariantClassification Always null. Interpretation Portal does not use variantClassification to classify variants
guidelineBasedVariantClassification GuidelineBasedVariantClassification Always null. Interpretation Portal does not use guidelineBasedVariantClassification to classify variants
algorithmBasedVariantClassifications array[AlgorithmBasedVariantClassification] Always null. Interpretation Portal does not use algorithmBasedVariantClassifications to classify variants
tier Tier Can be either Null, NONE, TIER1, TIER2, TIER3, TIER4, TIER5, TIERA, TIERB
domain Domain Always null. Domain not used for rare disease cases. 
"reportEvents": [
  {
    "reportEventId": "1678",
    "phenotypes": {"nonStandardPhenotype": ["Cystic renal disease"], "standardPhenotypes": null},
    "variantConsequences": [{"id": "SO:0001627","name": "intron_variant"},{"id": "SO:0001575","name": "splice_donor_variant"],
    "genePanel": {"panelIdentifier": "487","panelName": "Cystic renal disease","panelVersion": "3.19","source": "panelApp"},
    "modeOfInheritance": "biallelic",
    "genomicEntities":[{"type":"gene","ensemblId":"ENSG00000008710","geneSymbol":"PKD1","otherIds":null},{"type":"cytobands","ensemblId":null,"geneSymbol":null,"otherIds":[{"source":"cytoband","identifier":"p13.3"}]},
    "segregationPattern": "CompoundHeterozygous",
    "penetrance": "complete",
    "deNovoQualityScore": null,
    "fullyExplainsPhenotype": null,
    "groupOfVariants": 1362687230,
    "eventJustification": null,
    "roleInCancer": null,
    "actions": null,
    "score": null,
    "vendorSpecificScores": null,
    "variantClassification": null,
    "guidelineBasedVariantClassification": null,
    "algorithmBasedVariantClassifications": null,
    "tier": "TIER1",
    "domain": null
  }
],

IP RD ClinicalReport - GenomicEntity

Field Name Type Description
type* GenomicEntityType (enumeration) The type of the genomic entity.
ensemblId string Ensembl identifier for the feature.
geneSymbol string The HGNC gene symbol.
otherIds array[Identifier] Others identifiers for this genomic feature. Contains data source and ID. 
"genomicEntities": [
  {
    "type": "gene",
    "ensemblId": "ENSG00000008710",
    "geneSymbol": "PKD1",
    "otherIds": null
  },

IP RD ClinicalReport - VariantCall

Field Name Type Description
participantId* string Participant id
sampleId* string Sample id
zygosity* Zygosity(enumeration) Variant zygosity
phaseGenotype PhaseGenotype Always null. Interpretation Portal does not populate this field.
sampleVariantAlleleFrequency double Always null. Interpretation Portal does not populate this field.
depthReference integer Depth for Reference Allele
depthAlternate integer Depth for Alternate Allele
numberOfCopies array[NumberOfCopies] For copy number variants only. Number of copies of variant as reported by caller and confidence intervals.
alleleOrigins array[AlleleOrigin] (enumeration) List of applicable allele origin SO terms
supportingReadTypes SupportingReadType(enumeration) List of supporting read types, only for STRs. 
 "variantCalls": [
  {
    "participantId": "p999999999",
    "sampleId": "LP9000999-DNA_F96",
    "zygosity": "heterozygous",
    "phaseGenotype": null,
    "sampleVariantAlleleFrequency": null,
    "depthReference": null,
    "depthAlternate": null,
    "numberOfCopies": null,
    "alleleOrigins": ["germline_variant"],
    "supportingReadTypes": null
  }

IP RD ClinicalReport - VariantAttributes

Field Name Type Description
genomicChanges array[string] Always null. Interpretation Portal does not populate this field
cdnaChanges array[string] List of HGVS cDNA changes for the variant.
proteinChanges array[string] Always null. Interpretation Portal does not populate this field.
additionalTextualVariantAnnotations map[string] May contain additional information related to the variant, e.g. ClinVar annotations
references map[string] Always null. Interpretation Portal does not populate this field.
variantIdentifiers VariantIdentifiers This contains a dictionary to hold other variant identifiers. For Interpretation Portal clinical reports, this will contain dbSNP ID where relevant. It may also contain a reference to the variant in the VCF file in the otherIds field.
alleleFrequencies array[AlleleFrequency] This will contain population allele frequencies from external projects and/or internal GEL allele frequencies
additionalNumericVariantAnnotations map[float] Always null. rare disease tiering does not populate this field. Note this can be populated in older versions, but not for GMS cases
comments array[string] Comments entered by the reporter for this variant
alleleOrigins array[AlleleOrigin] Fixed value: ["germline_variant"]
ihp integer Always null. Interpretation Portal does not populate this field.
recurrentlyReported boolean Always null. Interpretation Portal does not populate this field.
fdp50 float Always null. Interpretation Portal does not populate this field.
others map[string] Always null. Interpretation Portal does not populate this field. 
{
"variantAttributes": {
      "genomicChanges": null,
      "cdnaChanges": ["ENST00000262304(ENSG00000008710):c.1849+1G>A","ENST00000423118(ENSG00000008710):c.1849+1G>A", "ENST00000568591(ENSG00000008710):c.*177+1G>A","ENST00000488185(ENSG00000008710):c.472+1498G>A"],
      "proteinChanges": [],
      "additionalTextualVariantAnnotations": null,
      "references": null,
      "variantIdentifiers": {"dbSnpId": null, "cosmicIds": null, "clinVarIds": null, "otherIds": [{"source": "VCF","identifier": "16_2115991_C"}]},
      "alleleFrequencies": null,
      "additionalNumericVariantAnnotations": null,
      "comments": ["example of a small variant level clinical report comment made in the Interpretation Portal"],
      "alleleOrigins": ["germline_variant"],
      "ihp": null,
      "recurrentlyReported": null,
      "fdp50": null,
      "others": null
    }
}

IP RD ClinicalReport - GenePanel

Field Name Type Description
panelIdentifier string Panel id used
panelName string Panel name used
panelVersion string Panel version
source string source is always PanelApp 
"genePanel": {
  "panelIdentifier": "487",
  "panelName": "Cystic renal disease",
  "panelVersion": "3.19",
  "source": "panelApp"
},

IP RD ClinicalReport - AlleleFrequency

Field Name Type Description
study* string The study from where this data comes from. See table.
population* string The specific population where this allele frequency belongs. See table.
alternateFrequency* float The frequency of the alternate allele 
      "alleleFrequencies": [
        {
          "study": "GEL",
          "population": "CNV_AF",
          "alternateFrequency": 0.0006478782
        },
        {
          "study": "GEL",
          "population": "CNV_AUC",
          "alternateFrequency": 0.0006478782
        }
      ],

IP RD ClinicalReport - VariantIdentifiers

Field Name Type Description
cosmicIds array[string] Always null. rare disease tiering does not populate this field
clinVarIds array[string] Always null. rare disease tiering does not populate this field
dbSnpId string Variant Identifier in dbSNP format e.g. rs17884070
otherIds array[Identifier] Rare disease tiering always fills in this field with one single element being the id of the variant obtain by concatenating the chromosome the position and the reference allele. 
"variantIdentifiers": {
    "dbSnpId": null,
    "cosmicIds": null,
    "clinVarIds": null,
    "otherIds": [
      {
        "source": "VCF",
        "identifier": "16_2115991_C"
      }
    ]
  },
Last update: 2023-03-01