type: allele_score 

table:
  filename: clinvar_20251019_chr.vcf.gz
  index_filename: clinvar_20251019_chr.vcf.gz.tbi

# score values
scores:
  - id: AF_ESP
    column_name: AF_ESP
    type: float
    desc: |
      allele frequencies from GO-ESP
    large_values_desc: "high frequency"
    small_values_desc: "low frequency"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True
               
  - id: AF_EXAC
    column_name: AF_EXAC
    type: float
    desc: |
      allele frequencies from ExAC
    large_values_desc: "high frequency"
    small_values_desc: "low frequency"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True     
      
  - id: AF_TGP
    column_name: AF_TGP
    type: float
    desc: |
      allele frequencies from TGP
    large_values_desc: "high frequency"
    small_values_desc: "low frequency"
    histogram:
      type: number
      number_of_bins: 100
      view_range:
        min: 0.0
        max: 1.0
      y_log_scale: True  
      
  - id: ALLELEID
    column_name: ALLELEID
    type: int
    desc: |
      ClinVar Allele ID
    histogram:
      type: number
      number_of_bins: 100
      
  - id: CLNDN
    column_name: CLNDN
    type: str
    desc: |
      ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True     
      displayed_values_count: 10
      label_rotation: 90
      
  - id: CLNDNINCL
    column_name: CLNDNINCL
    type: str
    desc: |
      For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True      
      
  - id: CLNDISDB
    column_name: CLNDISDB
    type: str
    desc: |
     Tag-value pairs of disease database name and identifier submitted for germline classifications, e.g. OMIM:NNNNNN"
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 

  - id: CLNDISDBINCL
    column_name: CLNDISDBINCL
    type: str
    desc: |
      For included Variant: Tag-value pairs of disease database name and identifier for germline classifications, e.g. OMIM:NNNNNN
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 

  - id: CLNREVSTAT
    column_name: CLNREVSTAT
    type: str
    desc: |
      ClinVar review status of germline classification for the Variation ID
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True  

  - id: CLNSIG
    column_name: CLNSIG
    type: str
    desc: |
      Aggregate germline classification for this single variant; multiple values are separated by a vertical bar
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 
      displayed_values_count: 20
      label_rotation: 90

  - id: CLNSIGCONF
    column_name: CLNSIGCONF
    type: str
    desc: |
      Conflicting germline classification for this single variant; multiple values are separated by a vertical bar
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 

  - id: CLNSIGINCL
    column_name: CLNSIGINCL
    type: str
    desc: |
      Germline classification for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:classification; multiple values are separated by a vertical bar
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 

  - id: CLNVC
    column_name: CLNVC
    type: str
    desc: |
      Variant type
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True 
      
  - id: CLNVCSO
    column_name: CLNVCSO
    type: str
    desc: |
      Sequence Ontology id for variant type
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True 

  - id: CLNVI
    column_name: CLNVI
    type: str
    desc: |
      the variant's clinical sources reported as tag-value pairs of database and variant identifier
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 
      
  - id: GENEINFO
    column_name: GENEINFO
    type: str
    desc: |
      Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 
 
  - id: MC
    column_name: MC
    type: str
    desc: |
      comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 
      
  - id: ONCDN
    column_name: ONCDN
    type: str
    desc: |
      ClinVar's preferred disease name for the concept specified by disease identifiers in ONCDISDB
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True  
  
  - id: ONCREVSTAT
    column_name: ONCREVSTAT
    type: str
    desc: |
      ClinVar review status of oncogenicity classification for the Variation ID
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True 
      
  - id: ONCDISDB
    column_name: ONCDISDB
    type: str
    desc: |
      Tag-value pairs of disease database name and identifier submitted for oncogenicity classifications, e.g. MedGen:NNNNNN
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True  
 
  - id: ONC
    column_name: ONC
    type: str
    desc: |
      Aggregate oncogenicity classification for this single variant; multiple values are separated by a vertical bar
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 

  - id: ORIGIN
    column_name: ORIGIN
    type: str
    desc: |
      Allele origin
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_origin"
      y_log_scale: True 
      
  - id: RS
    column_name: RS
    type: str
    desc: |
      Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)
    histogram:
      type: "null"
      reason: "Histogram is not available for this score."
       
  - id: SCIDN
    column_name: SCIDN
    type: str
    desc: |
      ClinVar's preferred disease name for the concept specified by disease identifiers in SCIDISDB
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True 
 
  - id: SCIDISDB
    column_name: SCIDISDB
    type: str
    desc: |
      Tag-value pairs of disease database name and identifier submitted for somatic clinial impact classifications, e.g. MedGen:NNNNNN
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_rightlabels"
      y_log_scale: True  
 
  - id: SCI
    column_name: SCI
    type: str
    desc: |
      Aggregate somatic clinical impact for this single variant; multiple values are separated by a vertical bar
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True 

  - id: SCIREVSTAT
    column_name: SCIREVSTAT
    type: str
    desc: |
      ClinVar review status of somatic clinical impact for the Variation ID
    histogram:
      type: categorical
      plot_function: "customplot1.py:plot_bottomlabels"
      y_log_scale: True 
      
      
default_annotation:
  - source: CLNSIG
    name: CLNSIG
  - source: CLNDN
    name: CLNDN

meta:
  summary: |
      Measure used to assess the clinical significance of genetic variants
  description: |

      [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) is a publicly available resource that collects and shares information 
      on the relationships between human genetic variants and their associated health conditions. 
      By providing detailed evidence and supporting data, ClinVar enables researchers, healthcare 
      professionals, and the broader medical community to better understand how specific 
      genetic variations impact health. Submissions to ClinVar include data from patient samples, 
      assessments of the clinical significance of variants, and information about the organizations 
      providing the data. All submitted variants are mapped to standardized reference sequences using 
      HGVS nomenclature. ClinVar supports both interactive exploration and integration 
      into clinical and research workflows, ensuring its data is accessible and useful for 
      the advancement of precision medicine. ClinVar actively collaborates with organizations 
      worldwide to address the evolving needs of the genetics and medical communities.
      
      [Landrum et al., ClinVar: public archive of interpretations of clinically relevant variants, 
      Nucleic Acids Research 2016](https://academic.oup.com/nar/article/44/D1/D862/2502702) 
      
      Downloaded on: 10/27/25 
      [https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/)
      
      Processing details: dataPrep.sh removes rows above header and remaps chromosome names to have `chr` prefix.
      
  labels:
    reference_genome: hg38/genomes/GRCh38-hg38