AI310-NM_007294.3-BRCA1-c.5297T>G

BRCA1 substitution on primary transcript

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="AI310"></f:id>
	<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"></nameType>
		<name value="NM_007294.3(BRCA1):c.5297T&gt;G"></name>
		<preferred value="true"></preferred>
	</alleleName>
	<alleleName>
		<nameType value="custom"></nameType>
		<name value="5416T&gt;G"></name>
	</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/RS213"></f:reference>
			<f:display value="NM_001014794.2"></f:display>
		</referenceSequence>
		<start>
			<index value="5529"></index>
		</start>
		<end>
			<index value="5530"></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>
	<related>
		<relatedType value="amino-acid-effect"></relatedType>
		<target>
			<f:reference value="ContextualAllele/AI312"></f:reference>
			<f:display value="NP_009225.1:p.Ile1766Ser"></f:display>
		</target>
	</related>
</ContextualAllele>

example: AI310-NM_007294.3-BRCA1-c.5297T>G.xml

schema: ContextualAllele.xsd

JSON

{
  "id": "AI310",
  "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": "NM_007294.3(BRCA1):c.5297T>G",
      "preferred": "true"
    },

    {
      "type": "custom",
      "name": "5416T>G"
    }
  ],

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

    "referenceSequence": 
    {
      "reference": "ReferenceSequence/RS213",
      "display": "NM_001014794.2"
    },

    "start": 
    {
      "index": "5528"
    },

    "end": 
    {
      "index": "5529"
    },

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

  "related": 
  [
    {
      "relatedType": "amino-acid-effect",
      "target": 
      {
        "reference": "ContextualAllele/AI312",
        "display": "NP_009225.1:p.Ile1766Ser"
      }
    }
  ]
}

example: AI310-NM_007294.3-BRCA1-c.5297T>G.json