AI302-NM_001014794.2-ILK-c.448+13A>G-b38

JSON-LD

{
  "@context": "http://clingen.org/models/ContextualAllele.jsonld",
  "@id": "http://clingendb.clingen.org/ContextualAllele/AI302",
  "@type": "ContextualAllele",
  "xref":
  [
    "http://clingen/alleleregistry/AI302"
  ],

  "canonicalAllele": "../../CanonicalAllele/CA401",

  "contextualAlleleType": "transcript",
  "allele": "G",
  "primaryNucleotideChangeType":
  {
    "@type": "PrimaryNucleotideChangeType",
    "@id": "http://www.sequenceontology.org/SO:1000002",
    "display": "substitution",
    "primary": "true"
  },

  "alleleName":
  [
    {
      "@type": "AlleleName",
      "nameType": "hgvs-cdna",
      "name": "NM_001014794.2:c.448+13A>G",
      "preferred": "true"
    }
  ],

  "referenceCoordinate":
  {
    "@type": "ReferenceCoordinate",
    "referenceSequence": "../../ReferenceSequence/RS201",
    "start": {
      "@type": "Position",
      "index" : "608",
      "externalOffsetLength":"12",
      "externalOffsetDirection":"+",
      "externalGenomicReferenceSequence": {
        "@type": "Reference",
        "reference": "../../ReferenceSequence/RS203",
        "display": "NC_000011.10"
      },
      "externalGenomicPositionIndex": "6608802"
    },
    "end": {
      "@type": "Position",
      "index" : "608",
      "externalOffsetLength":"13",
      "externalOffsetDirection":"+",
      "externalGenomicReferenceSequence": {
        "@type": "Reference",
        "reference": "../../ReferenceSequence/RS203",
        "display": "NC_000011.10"
      },
      "externalGenomicPositionIndex": "6608803"
    },
    "refAllele": "A",
    "primaryTranscriptRegionType":
    {
      "@type": "PrimaryTranscriptRegionType",
      "@id": "http://www.sequenceontology.org/SO:0000191",
      "display": "interior_intron",
    }
  }
}

example: AI302-NM_001014794.2-ILK-c.448+13A>G-b38.json

XML

<?xml version="1.0" encoding="UTF-8"?>
<ContextualAllele xmlns="http://clingen.org/dm/allele/v1"
	xmlns:f="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://clingen.org/dm/allele/v1 ../clingen-xsd/contextualallele.xsd ">
	<f:id value="AI302"></f:id>
	<canonicalAllele>
		<f:reference value="CanonicalAllele/CA401"></f:reference>
	</canonicalAllele>
	<contextualAlleleType value="transcript"></contextualAlleleType>
	<allele value="G"></allele>
	<primaryNucleotideChangeType>
		<f:coding>
			<f:system value="http://www.sequenceontology.org/"></f:system>
			<f:code value="SO:1000002"></f:code>
			<f:display value="substitution"></f:display>
			<f:primary value="true"></f:primary>
		</f:coding>
	</primaryNucleotideChangeType>
	<alleleName>
		<nameType value="hgvs-cdna"></nameType>
		<name value="NM_001014794.2:c.448+13A&gt;G"></name>
		<preferred value="true"></preferred>
	</alleleName>
	<referenceCoordinate>
		<referenceSequence>
			<f:reference value="ReferenceSequence/RS201"></f:reference>
			<f:display value="NM_001014794.2"></f:display>
		</referenceSequence>
		<start>
			<index value="608"></index>
			<externalOffsetLength value="12"></externalOffsetLength>
			<externalOffsetDirection value="+"></externalOffsetDirection>
			<externalGenomicReferenceSequence>
				<f:reference value="ReferenceSequence/RS203"></f:reference>
				<f:display value="NC_000011.10"></f:display>
			</externalGenomicReferenceSequence>
			<externalGenomicPositionIndex value="6608803"></externalGenomicPositionIndex>
		</start>
		<end>
			<index value="608"></index>
			<externalOffsetLength value="13"></externalOffsetLength>
			<externalOffsetDirection value="+"></externalOffsetDirection>
			<externalGenomicReferenceSequence>
				<f:reference value="ReferenceSequence/RS203"></f:reference>
				<f:display value="NC_000011.10"></f:display>
			</externalGenomicReferenceSequence>
			<externalGenomicPositionIndex value="6608804"></externalGenomicPositionIndex>
		</end>
		<refAllele value="A"></refAllele>
		<primaryTranscriptRegionType>
			<f:coding>
				<f:system value="http://www.sequenceontology.org/"></f:system>
				<f:code value="SO:0000191"></f:code>
				<f:display value="interior_intron"></f:display>
			</f:coding>
		</primaryTranscriptRegionType>
	</referenceCoordinate>

</ContextualAllele>

example: AI302-NM_001014794.2-ILK-c.448+13A>G-b38.xml

schema: ContextualAllele.xsd

JSON

{
  "id": "AI302",
  "canonicalAllele": 
  {
    "reference": "CanonicalAllele/CA401"
  },

  "contextualAlleleType": "transcript",
  "allele": "G",
  "primaryNucleotideChangeType": 
  {
    "coding": 
    [
      {
        "system": "http://www.sequenceontology.org/",
        "code": "SO:1000002",
        "display": "substitution",
        "primary": "true"
      }
    ]
  },

  "alleleName": 
  [
    {
      "nameType": "hgvs-cdna",
      "name": "NM_001014794.2:c.448+13A>G",
      "preferred": "true"
    }
  ],

  "referenceCoordinate": 
  {
    "referenceSequence": 
    {
      "reference": "/ReferenceSequence/RS201",
      "display": "NM_001014794.2"
    },

    "start": 
    {
      "index": "608",
      "externalOffsetLength": "12",
      "externalOffsetDirection": "+",
      "externalGenomicReferenceSequence": 
      {
        "reference": "ReferenceSequence/RS203",
        "display": "NC_000011.10"
      },

      "externalGenomicPositionIndex": "6608802"
    },

    "end": 
    {
      "index": "608",
      "externalOffsetEnd": "13",
      "externalOffsetDirection": "+",
      "externalGenomicReferenceSequence": 
      {
        "reference": "ReferenceSequence/RS203",
        "display": "NC_000011.10"
      },

      "externalGenomicPositionIndex": "6608803"
    },

    "refAllele": "A",
    "primaryTranscriptRegionType": 
    {
      "coding": 
      [
        {
          "system": "http://www.sequenceontology.org/",
          "code": "SO:0000191",
          "display": "interior_intron"
        }
      ]
    }
  }
}

example: AI302-NM_001014794.2-ILK-c.448+13A>G-b38.json