clingen-json

"clingen":[
   {
      "chromosome":"17",
      "begin":525,
      "end":14667519,
      "variantType":"copy_number_gain",
      "id":"nsv996083",
      "clinicalInterpretation":"pathogenic",
      "observedGains":1,
      "validated":true,
      "phenotypes":[
         "Intrauterine growth retardation"
      ],
      "phenotypeIds":[
         "HP:0001511",
         "MedGen:C1853481"
      ],
      "reciprocalOverlap":0.00131
   },
   {
      "chromosome":"17",
      "begin":45835,
      "end":7600330,
      "variantType":"copy_number_loss",
      "id":"nsv869419",
      "clinicalInterpretation":"pathogenic",
      "observedLosses":1,
      "validated":true,
      "phenotypes":[
         "Developmental delay AND/OR other significant developmental or morphological phenotypes"
      ],
      "reciprocalOverlap":0.00254
   }
]

Field	Type	Notes
clingen	object array
chromosome	string	Ensembl-style chromosome names
begin	integer	1-based position
end	integer	1-based position
variantType	string	Any of the sequence alterations defined here.
id	string	Identifier from the data source. Alternatively a VID
clinicalInterpretation	string	see possible values below
observedGains	integer	Range: 0 - (231 - 1). Only used if copy_number_variation, copy_number_loss, or copy_number_gain.
observedLosses	integer	Range: 0 - (231 - 1). Only used if copy_number_variation, copy_number_loss, or copy_number_gain.
validated	boolean
phenotypes	string array	Description of the phenotype.
phenotypeIds	string array	Description of the phenotype IDs.
reciprocalOverlap	floating point	Range: 0 - 1. E.g. 0.57 would indicate a 57% reciprocal overlap. Specified up to 5 decimal places (Not reported for Insertions).

clinicalInterpretation

• benign
• curated benign
• curated pathogenic
• likely benign
• likely pathogenic
• path gain
• path loss
• pathogenic
• uncertain