AI318-LRG_292t1-BRCA1-c.5297T>G

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="AI318"></f:id>
	<identifier>
		<f:system value="http://www.ncbi.nlm.nih.gov/clinvar/variation"></f:system>
		<f:value value="37656"></f:value>
	</identifier>
	<canonicalAllele>
		<f:reference value="CanonicalAllele/CA402"></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" />
		<name value="LRG_292t1:c.5297T&gt;G" />
		<preferred value="true" />
	</alleleName>
	<referenceCoordinate>
		<identifier>
			<f:system value="http://www.ncbi.nlm.nih.gov/snp"></f:system>
			<f:value value="80357463"></f:value>
		</identifier>
		<referenceSequence>
			<f:reference value="ReferenceSequence/RS217"></f:reference>
			<f:display value="LRG_292t1"></f:display>
		</referenceSequence>
    <start>
      <index value="5296"></index>
    </start>
    <end>
      <index value="5297"></index>
    </end>
		<refAllele value="T"></refAllele>
		<primaryTranscriptRegionType>
			<f:coding>
				<f:system value="http://www.sequenceontology.org/"></f:system>
				<f:code value="SO:0000316"></f:code>
				<f:display value="CDS"></f:display>
			</f:coding>
		</primaryTranscriptRegionType>
	</referenceCoordinate>

</ContextualAllele>

example: AI318-LRG_292t1-BRCA1-c.5297T>G.xml

schema: ContextualAllele.xsd

JSON

{
  "id": "AI318",
  "canonicalAllele": 
  {
    "reference": "CanonicalAllele/CA402"
  },

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

  "alleleName": 
  [
    {
      "nameType": "hgvs-cdna",
      "name": "LRG_292t1:c.5297T>G",
      "preferred": "true"
    }
  ],

  "referenceCoordinate": 
  {
    "identifier": 
    [
      {
        "system": "http://www.ncbi.nlm.nih.gov/snp",
        "value": "80357463"
      }
    ],

    "referenceSequence": 
    {
      "reference": "ReferenceSequence/RS217",
      "display": "LRG_292t1"
    },

    "start": 
    {
      "index": "5296"
    },

    "end": 
    {
      "index": "5297"
    },

    "refAllele": "T",
    "primaryTranscriptRegionType": 
    {
      "coding": 
      [
        {
          "system": "http://www.sequenceontology.org/",
          "code": "SO:0000316",
          "display": "CDS"
        }
      ]
    }
  }
}

example: AI318-LRG_292t1-BRCA1-c.5297T>G.json