Package org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity

Class ClinVarData

java.lang.Object
org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
public class ClinVarData extends Object
Immutable data class representing data from the ClinVar resource, with explanation of the data from https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/
Since:
10.1.0
Author:
Jules Jacobsen <j.jacobsen@qmul.ac.uk>

  • Method Details

    • empty

      public static ClinVarData empty()

    • isEmpty

      public boolean isEmpty()

    • getVariationId

      public String getVariationId()

    • getPrimaryInterpretation

      public ClinVarData.ClinSig getPrimaryInterpretation()

    • getConflictingInterpretationCounts

      public Map<ClinVarData.ClinSig,Integer> getConflictingInterpretationCounts()

    • getSecondaryInterpretations

      public Set<ClinVarData.ClinSig> getSecondaryInterpretations()

    • getReviewStatus

      public ClinVarData.ReviewStatus getReviewStatus()

    • getIncludedAlleles

      public Map<String,ClinVarData.ClinSig> getIncludedAlleles()

    • getGeneSymbol

      public String getGeneSymbol()

    • getVariantEffect

      public de.charite.compbio.jannovar.annotation.VariantEffect getVariantEffect()

    • getHgvsCdna

      public String getHgvsCdna()

    • getHgvsProtein

      public String getHgvsProtein()

    • isSecondaryAssociationRiskFactorOrOther

      public boolean isSecondaryAssociationRiskFactorOrOther()
      Returns:
      true if the secondary CLNSIG contains one of 'affects', 'other', 'association', 'risk factor' or 'protective'. These are considered unimportant from the mendelian disease perspective. The category 'drug response' is *not* included here as these are also associated with CFTR alleles known to be pathogenic/likely pathogenic for CF.
      Since:
      13.0.0

    • starRating

      public int starRating()
      Returns the ClinVar star rating. In the VCF CLNREVSTAT the star ratings are mapped as follows: 

       1* criteria_provided,_conflicting_interpretations
 1* criteria_provided,_single_submitter
 2* criteria_provided,_multiple_submitters,_no_conflicts
 3* reviewed_by_expert_panel
 4* practice_guideline
      Returns:
      an integer value between 0 (worst) and 4 (best)
      Since:
      13.0.0

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toBuilder

      public ClinVarData.Builder toBuilder()

    • builder

      public static ClinVarData.Builder builder()