AI312-NP_009225.1-BRCA1-p.Ile1766Ser

BRCA1 missense amino acid variant Ile1766Ser

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="AI312"></f:id>
	<identifier>
		<f:system value="http://clingen.org/alleleregistry"></f:system>
		<f:value value="AI312"></f:value>
	</identifier>
	<canonicalAllele>
		<f:reference value="CanonicalAllele/CA403"></f:reference>
	</canonicalAllele>
	<contextualAlleleType value="amino acid"></contextualAlleleType>
	<allele value="Ser"></allele>
	<primaryAminoAcidChangeType>
		<f:coding>
			<f:system value="http://www.sequenceontology.org/"></f:system>
			<f:code value="SO:0001583"></f:code>
			<f:display value="missense variant"></f:display>
		</f:coding>
	</primaryAminoAcidChangeType>
	<alleleName>
		<nameType value="hgvs-protein-3"></nameType>
		<name value="p.Ile1766Ser"></name>
	</alleleName>
	<alleleName>
		<nameType value="custom"></nameType>
		<name value="I1766S"></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/RS214"></f:reference>
			<f:display value="NP_009225.1"></f:display>
		</referenceSequence>
		<start>
			<index value="1765"></index>
		</start>
		<end>
			<index value="1766"></index>
		</end>
		<refAllele value="Ile"></refAllele>
	</referenceCoordinate>
	<related>
		<relatedType value="transcript-allele-cause"></relatedType>
		<target>
			<f:reference value="ContextualAllele/AI310"></f:reference>
			<f:display value="NM_007294.3(BRCA1):c.5297T&gt;G"></f:display>
		</target>
	</related>

</ContextualAllele>

example: AI312-NP_009225.1-BRCA1-p.Ile1766Ser.xml

schema: ContextualAllele.xsd

JSON

{
  "id": "AI312",
  "canonicalAllele": 
  {
    "reference": "CanonicalAllele/CA403"
  },

  "contextualAlleleType": "amino-acid",
  "allele": "Ser",
  "primaryAminoAcidChangeType": 
  {
    "coding": 
    [
      {
        "system": "http://www.sequenceontology.org/",
        "code": "SO:0001583",
        "display": "missense variant"
      }
    ]
  },

  "alleleName": 
  [
    {
      "nameType": "hgvs-protein-3",
      "name": "p.Ile1766Ser"
    },

    {
      "nameType": "hgvs-protein-1",
      "name": "I1766S"
    }
  ],

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

    "referenceSequence": 
    {
      "reference": "ReferenceSequence/RS214",
      "display": "NP_009225.1"
    },

    "start": 
    {
      "index": "1765"
    },

    "end": 
    {
      "index": "1766"
    },

    "refAllele": "Ile"
  },

  "related": 
  [
    {
      "relatedType": "transcript-allele-cause",
      "target": 
      {
        "reference": "ContextualAllele/AI310",
        "display": "NM_007294.3(BRCA1):c.5297T>G"
      }
    }
  ]
}

example: AI312-NP_009225.1-BRCA1-p.Ile1766Ser.json