From b7a00605c33edd656bea4d53086ae4559117740c Mon Sep 17 00:00:00 2001
From: dglemos <dlemos@ebi.ac.uk>
Date: Thu, 15 Jun 2023 15:11:55 +0100
Subject: [PATCH 1/2] Add pathogenicityPredictions and allele to frequency

---
 .../genomicVariations/defaultSchema.json            | 13 +++++++++++++
 .../genomicVariations/defaultSchema.yaml            |  9 +++++++++
 2 files changed, 22 insertions(+)

diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
index c07edcc85..ac260a362 100644
--- 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/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
index 2e66e4fd0..c00c026d0 100644
--- 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:

From 56c4a40360fc7faf718eabd38b2d148316ec82b0 Mon Sep 17 00:00:00 2001
From: dglemos <dlemos@ebi.ac.uk>
Date: Thu, 15 Jun 2023 15:40:25 +0100
Subject: [PATCH 2/2] Add example

---
 .../examples/genomicVariant-MID-example.json          | 11 +++++++++++
 .../examples/genomicVariant-MID-example.yaml          |  6 ++++++
 2 files changed, 17 insertions(+)

diff --git a/models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json b/models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json
index 1322d2192..79f897471 100644
--- a/models/json/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.json
+++ b/models/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/examples/genomicVariant-MID-example.yaml b/models/src/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.yaml
index 1a350c9e3..329e991bf 100644
--- a/models/src/beacon-v2-default-model/genomicVariations/examples/genomicVariant-MID-example.yaml
+++ b/models/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/