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PredictedVariantConsequence

Class for predicted consequences and associated data from VEP analysis of a VariantGenomicLocationAssociation

classDiagram AuditedObject <|-- PredictedVariantConsequence PredictedVariantConsequence : amino_acid_reference PredictedVariantConsequence : amino_acid_variant PredictedVariantConsequence : calculated_cdna_end PredictedVariantConsequence : calculated_cdna_start PredictedVariantConsequence : calculated_cds_end PredictedVariantConsequence : calculated_cds_start PredictedVariantConsequence : calculated_protein_end PredictedVariantConsequence : calculated_protein_start PredictedVariantConsequence : codon_reference PredictedVariantConsequence : codon_variant PredictedVariantConsequence : created_by PredictedVariantConsequence : date_created PredictedVariantConsequence : date_updated PredictedVariantConsequence : db_date_created PredictedVariantConsequence : db_date_updated PredictedVariantConsequence : gene_level_consequence PredictedVariantConsequence : hgvs_coding_nomenclature PredictedVariantConsequence : hgvs_protein_nomenclature PredictedVariantConsequence : internal PredictedVariantConsequence : obsolete PredictedVariantConsequence : polyphen_prediction PredictedVariantConsequence : polyphen_score PredictedVariantConsequence : sift_prediction PredictedVariantConsequence : sift_score PredictedVariantConsequence : updated_by PredictedVariantConsequence : variant_genomic_location PredictedVariantConsequence : variant_transcript PredictedVariantConsequence : vep_consequences PredictedVariantConsequence : vep_impact

URI: alliance:PredictedVariantConsequence

Parent Classes

Slots

Name Description
amino_acid_reference reference genome amino acid sequence at variant position
amino_acid_variant variant amino acid sequence at variant position
calculated_cdna_end end position of variation in cDNA coordinates as calculated by VEP from input VCF, GFF and BAM files
calculated_cdna_start start position of variation in cDNA coordinates as calculated by VEP from input VCF, GFF and BAM files
calculated_cds_end end position of variation in CDS coordinates as calculated by VEP from input VCF, GFF and BAM files
calculated_cds_start start position of variation in CDS coordinates as calculated by VEP from input VCF, GFF and BAM files
calculated_protein_end end position of variation in protein amino acid coordinates as calculated by VEP from input VCF, GFF and BAM files
calculated_protein_start start position of variation in protein amino acid coordinates as calculated by VEP from input VCF, GFF and BAM files
codon_reference reference sequence of codon(s) affected by variation - bases outside of the variant region are in lower case, those within are in upper case (e.g. cTa)
codon_variant variant sequence of codon(s) affected by variation - bases outside of the variant region are in lower case, those within are in upper case (e.g. cAa)
created_by The individual that created the entity.
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
gene_level_consequence Boolean indicating whether transcript consequence is the most severe consequence for the corresponding gene. In the case of equally severe consequences, a single transcript consequence will be designated as the gene-level consequence by the VEP
hgvs_coding_nomenclature HGVSc nomenclature for variation in coding sequence
hgvs_protein_nomenclature HGVSp nomenclature for variation in protein
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
polyphen_prediction PolyPhen-2 prediction
polyphen_score PolyPhen-2 score between 0 and 1
sift_prediction SIFT prediction
sift_score SIFT score between 0 and 1
updated_by The individual that last modified the entity.
variant_genomic_location VariantGenomicLocationAssociation for which consequences are calculated
variant_transcript Transcript to which variant effect prediction applies
vep_consequences VEP consequence
vep_impact VEP predicted impact of variation on molecule

Mappings

Mapping Type Mapped Value
self ['alliance:PredictedVariantConsequence']
native ['alliance:PredictedVariantConsequence']

LinkML Specification

Direct

name: PredictedVariantConsequence
description: Class for predicted consequences and associated data from VEP analysis
  of a VariantGenomicLocationAssociation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  variant_genomic_location:
    name: variant_genomic_location
    description: VariantGenomicLocationAssociation for which consequences are calculated
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: VariantGenomicLocationAssociation
    required: true
  variant_transcript:
    name: variant_transcript
    description: Transcript to which variant effect prediction applies
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: Transcript
    required: true
  vep_impact:
    name: vep_impact
    description: VEP predicted impact of variation on molecule
    notes:
    - 'permissible_values: high, moderate, low, modifier'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: VocabularyTerm
    required: true
  vep_consequences:
    name: vep_consequences
    description: VEP consequence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    multivalued: true
    range: SOTerm
    required: true
  polyphen_score:
    name: polyphen_score
    description: PolyPhen-2 score between 0 and 1
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: float
  polyphen_prediction:
    name: polyphen_prediction
    description: PolyPhen-2 prediction
    notes:
    - 'permissible_values: possibly_damaging, probably_damaging, benign'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: VocabularyTerm
  sift_score:
    name: sift_score
    description: SIFT score between 0 and 1
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: float
  sift_prediction:
    name: sift_prediction
    description: SIFT prediction
    notes:
    - 'permissible_values: deleterious, tolerated'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: VocabularyTerm
  amino_acid_reference:
    name: amino_acid_reference
    description: reference genome amino acid sequence at variant position
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  amino_acid_variant:
    name: amino_acid_variant
    description: variant amino acid sequence at variant position
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  codon_reference:
    name: codon_reference
    description: reference sequence of codon(s) affected by variation - bases outside
      of the variant region are in lower case, those within are in upper case (e.g.
      cTa)
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  codon_variant:
    name: codon_variant
    description: variant sequence of codon(s) affected by variation - bases outside
      of the variant region are in lower case, those within are in upper case (e.g.
      cAa)
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  calculated_cdna_start:
    name: calculated_cdna_start
    description: start position of variation in cDNA coordinates as calculated by
      VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  calculated_cdna_end:
    name: calculated_cdna_end
    description: end position of variation in cDNA coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  calculated_cds_start:
    name: calculated_cds_start
    description: start position of variation in CDS coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  calculated_cds_end:
    name: calculated_cds_end
    description: end position of variation in CDS coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  calculated_protein_start:
    name: calculated_protein_start
    description: start position of variation in protein amino acid coordinates as
      calculated by VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  calculated_protein_end:
    name: calculated_protein_end
    description: end position of variation in protein amino acid coordinates as calculated
      by VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: integer
  hgvs_protein_nomenclature:
    name: hgvs_protein_nomenclature
    description: HGVSp nomenclature for variation in protein
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  hgvs_coding_nomenclature:
    name: hgvs_coding_nomenclature
    description: HGVSc nomenclature for variation in coding sequence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: string
  gene_level_consequence:
    name: gene_level_consequence
    description: Boolean indicating whether transcript consequence is the most severe
      consequence for the corresponding gene.  In the case of equally severe consequences,
      a single transcript consequence will be designated as the  gene-level consequence
      by the VEP
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    range: boolean
    required: true

Induced

name: PredictedVariantConsequence
description: Class for predicted consequences and associated data from VEP analysis
  of a VariantGenomicLocationAssociation
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
attributes:
  variant_genomic_location:
    name: variant_genomic_location
    description: VariantGenomicLocationAssociation for which consequences are calculated
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: variant_genomic_location
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: VariantGenomicLocationAssociation
    required: true
  variant_transcript:
    name: variant_transcript
    description: Transcript to which variant effect prediction applies
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: variant_transcript
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: Transcript
    required: true
  vep_impact:
    name: vep_impact
    description: VEP predicted impact of variation on molecule
    notes:
    - 'permissible_values: high, moderate, low, modifier'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: vep_impact
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: VocabularyTerm
    required: true
  vep_consequences:
    name: vep_consequences
    description: VEP consequence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    multivalued: true
    alias: vep_consequences
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: SOTerm
    required: true
  polyphen_score:
    name: polyphen_score
    description: PolyPhen-2 score between 0 and 1
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: polyphen_score
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: float
  polyphen_prediction:
    name: polyphen_prediction
    description: PolyPhen-2 prediction
    notes:
    - 'permissible_values: possibly_damaging, probably_damaging, benign'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: polyphen_prediction
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: VocabularyTerm
  sift_score:
    name: sift_score
    description: SIFT score between 0 and 1
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: sift_score
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: float
  sift_prediction:
    name: sift_prediction
    description: SIFT prediction
    notes:
    - 'permissible_values: deleterious, tolerated'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: sift_prediction
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: VocabularyTerm
  amino_acid_reference:
    name: amino_acid_reference
    description: reference genome amino acid sequence at variant position
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: amino_acid_reference
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  amino_acid_variant:
    name: amino_acid_variant
    description: variant amino acid sequence at variant position
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: amino_acid_variant
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  codon_reference:
    name: codon_reference
    description: reference sequence of codon(s) affected by variation - bases outside
      of the variant region are in lower case, those within are in upper case (e.g.
      cTa)
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: codon_reference
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  codon_variant:
    name: codon_variant
    description: variant sequence of codon(s) affected by variation - bases outside
      of the variant region are in lower case, those within are in upper case (e.g.
      cAa)
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: codon_variant
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  calculated_cdna_start:
    name: calculated_cdna_start
    description: start position of variation in cDNA coordinates as calculated by
      VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_cdna_start
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  calculated_cdna_end:
    name: calculated_cdna_end
    description: end position of variation in cDNA coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_cdna_end
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  calculated_cds_start:
    name: calculated_cds_start
    description: start position of variation in CDS coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_cds_start
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  calculated_cds_end:
    name: calculated_cds_end
    description: end position of variation in CDS coordinates as calculated by VEP
      from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_cds_end
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  calculated_protein_start:
    name: calculated_protein_start
    description: start position of variation in protein amino acid coordinates as
      calculated by VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_protein_start
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  calculated_protein_end:
    name: calculated_protein_end
    description: end position of variation in protein amino acid coordinates as calculated
      by VEP from input VCF, GFF and BAM files
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: calculated_protein_end
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: integer
  hgvs_protein_nomenclature:
    name: hgvs_protein_nomenclature
    description: HGVSp nomenclature for variation in protein
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: hgvs_protein_nomenclature
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  hgvs_coding_nomenclature:
    name: hgvs_coding_nomenclature
    description: HGVSc nomenclature for variation in coding sequence
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: hgvs_coding_nomenclature
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: string
  gene_level_consequence:
    name: gene_level_consequence
    description: Boolean indicating whether transcript consequence is the most severe
      consequence for the corresponding gene.  In the case of equally severe consequences,
      a single transcript consequence will be designated as the  gene-level consequence
      by the VEP
    from_schema: https://github.com/alliance-genome/agr_curation_schema/src/schema/variantConsequence
    alias: gene_level_consequence
    owner: PredictedVariantConsequence
    domain_of:
    - PredictedVariantConsequence
    range: boolean
    required: true
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: PredictedVariantConsequence
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean