Merge pull request #101 from ga4gh-beacon/genomicVariations_add-patho…

…genicity-predictions Genomic variations add pathogenicity predictions
ga4gh-beacon · Jul 17, 2023 · 4ce7b1d · 4ce7b1d
2 parents e7d7962 + 56c4a40
commit 4ce7b1d
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diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
@@ -441,6 +441,13 @@
         },
         "PopulationFrequency": {
             "properties": {
+                "allele": {
+                    "description": "Specific allele associated with the frequency.",
+                    "examples": [
+                        "A"
+                    ],
+                    "type": "string"
+                },
                 "alleleFrequency": {
                     "description": "Allele frequency between 0 and 1.",
                     "examples": [
@@ -512,6 +519,12 @@
                     },
                     "type": "array"
                 },
+                "pathogenicityPredictions": {
+                    "items": {
+                        "$ref": "#/definitions/PhenoClinicEffect"
+                    },
+                    "type": "array"
+                },
                 "phenotypicEffects": {
                     "items": {
                         "$ref": "#/definitions/PhenoClinicEffect"

diff --git a/...s/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json b/...s/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json
@@ -95,6 +95,17 @@
                     "label": "hypercholesterolemia, autosomal dominant, 3"
                 }
             }
+        ],
+        "pathogenicityPredictions": [
+            {
+                "annotatedWith": {
+                    "toolName": "Combined Annotation-Dependent Depletion (CADD)",
+                    "version": "v1.6"
+                },
+                "effect": {
+                    "id": "phred_score:0.381"
+                }
+            }
         ]
     },
     "variation": {

diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
@@ -321,6 +321,11 @@ definitions:
         description: Allele frequency between 0 and 1.
         examples:
           - 3.186e-05
+      allele:
+        type: string
+        description: Specific allele associated with the frequency.
+        examples:
+          - A
     required:
       - population
       - alleleFrequency
@@ -412,6 +417,10 @@ definitions:
         type: array
         items:
           $ref: '#/definitions/PhenoClinicEffect'
+      pathogenicityPredictions:
+        type: array
+        items:
+          $ref: '#/definitions/PhenoClinicEffect'
   SoftwareTool:
     type: object
     properties:

diff --git a/...ls/src/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.yaml b/...ls/src/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.yaml
@@ -54,6 +54,12 @@ variantLevelData:
         id: MONDO:0011369
         label: hypercholesterolemia, autosomal dominant, 3
       clinicalRelevance: uncertain significance
+  pathogenicityPredictions:
+    - annotatedWith:
+        version: v1.6
+        toolName: Combined Annotation-Dependent Depletion (CADD)
+      effect:
+        id: phred_score:0.381
 frequencyInPopulations:
   - source: gnomaD Genomes
     sourceReference: https://gnomad.broadinstitute.org/