Type: object
Description: A variant allele. Alleles can be listed using HGVS, VCF, SPDI or ISCN notation. SPDI format is the exchange standard used for ClinVar, dbSNP and soon the EVA Tools for interconversion between SPDI, HGVS and VCF exist at https://api.ncbi.nlm.nih.gov/variation/v0/

Properties

hgvsAllele

• type: https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/HgvsAllele.json [LINK]

HGVS version of describing a sequence variation

hgvsAllele Value Example

"add example"

iscnAllele

• type: https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/IscnAllele.json [LINK]

Cytogenetic variation in ISCN format

iscnAllele Value Example

"t(8;14)(q24;q32)"

spdiAllele

• type: https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/SpdiAllele.json [LINK]

add description

spdiAllele Value Example

{
   "deletedSequence" : "T",
   "id" : "id_abc_123",
   "insertedSequence" : "G",
   "position" : "123256214",
   "seqId" : "NC_000010.10"
}

vcfAllele

• type: https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/VcfAllele.json [LINK]

add description

vcfAllele Value Example

{
   "alt" : "G",
   "chr" : "10",
   "genomeAssembly" : "GRCh37",
   "pos" : "123256215",
   "ref" : "T"
}

zygosity

• type: https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [LINK]

add description

zygosity Value Example

{
   "id" : "GENO:0000135",
   "label" : "heterozygous"
}

Variant Value Example

{
   "description" : "description of variant",
   "id" : "ID_12345",
   "vcfAllele" : {
      "alt" : "G",
      "chr" : "10",
      "genomeAssembly" : "GRCh37",
      "pos" : "123256215",
      "ref" : "T"
   }
}