Variant sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

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

Property Type
hgvsAllele https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/HgvsAllele.json [SRC] [HTML]
iscnAllele https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/IscnAllele.json [SRC] [HTML]
spdiAllele https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/SpdiAllele.json [SRC] [HTML]
vcfAllele https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/VcfAllele.json [SRC] [HTML]
zygosity https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]

hgvsAllele

HGVS version of describing a sequence variation

hgvsAllele Value Example
"add example"

iscnAllele

Cytogenetic variation in ISCN format

iscnAllele Value Example
"t(8;14)(q24;q32)"

spdiAllele

add description

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

vcfAllele

add description

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

zygosity

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"
   }
}