dipper.models.ClinVarRecord module

https://www.ncbi.nlm.nih.gov/clinvar/docs/details/ Object mapping to XML schema

class dipper.models.ClinVarRecord.Allele(id: str, label: Optional[str] = None, variant_type: Optional[str] = None, genes: Optional[List[dipper.models.ClinVarRecord.Gene]] = None, synonyms: Optional[List[str]] = None, dbsnps: Optional[List[str]] = None)

Bases: object

ClinVar Allele Alleles can have 0 to many genes

These are called alleles and variants on the ClinVar UI, and variant, single nucleotide variant, etc in the XML

id: allele id label: label variant_type: single nucleotide variant genes: gene(s) in which the variant is found synonyms: eg HGVC dbsnp: dbSNP curies

class dipper.models.ClinVarRecord.ClinVarRecord(id: str, accession: str, created: str, updated: str, genovar: dipper.models.ClinVarRecord.Genovar, significance: str, conditions: Optional[List[dipper.models.ClinVarRecord.Condition]] = None)

Bases: object

Reference ClinVar Record (RCV) id: RCV id accession: RCV accession (eg RCV000123456) created: Created date updated: Updated date genovar: the variant or genotype associated with the condition(s) significance: clinical significance (eg benign, pathogenic) condition: The condition(s) for which this allele set was interpreted, with

links to databases with defining information about that condition.

class dipper.models.ClinVarRecord.Condition(id: str, label: Optional[str] = None, database: Optional[str] = None, medgen_id: Optional[str] = None)

Bases: object

ClinVar condition

class dipper.models.ClinVarRecord.Gene(id: Union[str, int, None], association_to_allele: str)

Bases: object

ClinVar Gene Intentionally leaves out label/symbol, this should come from HGNC

class dipper.models.ClinVarRecord.Genotype(id: str, label: Optional[str] = None, variants: Optional[List[dipper.models.ClinVarRecord.Variant]] = None, variant_type: Optional[str] = None)

Bases: dipper.models.ClinVarRecord.Genovar

ClinVar genotype Example: Compound Heterozygote, Diplotype

These are called variants on the ClinVar UI, and a GenotypeSet in the XML

class dipper.models.ClinVarRecord.Genovar(id: str, label: Optional[str] = None, variant_type: Optional[str] = None)

Bases: object

Sequence feature entity that is linked to a disease in an Reference ClinVar Record, it is either a Variant or Genotype

class dipper.models.ClinVarRecord.Variant(id: str, label: Optional[str] = None, alleles: Optional[List[dipper.models.ClinVarRecord.Allele]] = None, variant_type: Optional[str] = None)

Bases: dipper.models.ClinVarRecord.Genovar

ClinVar variant, variants can have one or more alleles

These are called variants and alleles on the ClinVar UI, and Variants in the XML