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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data Description

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

Data DescriptionExample Response

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 ¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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¶

Data DescriptionExample Response

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

Interpretation Portal Clinical Report Data

IP RD ClinicalReport¶

IP RD ClinicalReport - SmallVariant¶

IP RD ClinicalReport - StructuralVariant¶

IP RD ClinicalReport - ShortTandemRepeat¶

IP RD ClinicalReport - STR Coordinates¶

IP RD ClinicalReport - VariantCoordinates¶

IP RD ClinicalReport - ReportEvent¶

IP RD ClinicalReport - GenomicEntity¶

IP RD ClinicalReport - VariantCall¶

IP RD ClinicalReport - VariantAttributes¶

IP RD ClinicalReport - GenePanel¶

IP RD ClinicalReport - AlleleFrequency¶

IP RD ClinicalReport - VariantIdentifiers¶

IP RD ClinicalReport - STR Coordinates ¶

IP RD ClinicalReport - VariantCoordinates ¶