GA4GH Variant Annotation Specification
Introduction
Overview
Components
Use Cases and Implementations
Scope and Development
Modeling Foundations
Core Class Hierarchy
Data Structures
Statement Structure
Evidence Line Structure
Study Result Structure
Role of Propositions
Propositions in Statements
Propositions in Evidence Lines
Profiles
Profiling Tasks
Profiling Example
VA Core Model
Entity
Information Entity
Method
Document
Data Set
Statement
Evidence Line
Study Result
Contribution
Agent
Study Group
Proposition
Element
Coding
Concept Mapping
Mappable Concept
Extension
Data Types
code
iriReference
date
datetime
Domain Entities
Variation
Condition
Condition Set
Therapeutic
Therapy Group
Gene
VA Profiles
Base Profiles
Proposition Profiles
Variant Pathogenicity Proposition
Variant Oncogenicity Proposition
Variant Clinical Significance Proposition
Variant Therapeutic Response Proposition
Variant Diagnostic Proposition
Variant Prognostic Proposition
Experimental Variant Functional Impact Proposition
Study Result Profiles
Cohort Allele Frequency Study Result
Experimental Variant Functional Impact Study Result
Community Profiles
ACMG 2015 Aligned Profiles
Variant Pathogenicity Statement (ACMG 2015)
Variant Pathogenicity Evidence Line (ACMG 2015)
CCV 2022 Aligned Profiles
Variant Oncogenicity Statement (CCV 2022)
Variant Oncogenicity Evidence Line (CCV 2022)
AMP/ASCO/CAP 2017 Aligned Profiles
Variant Clinical Significance Statement
JSON Schema Catalog
Reference Implementation
Developer Guide
Profile Definition Mechanisms
Authoring Base vs Community Profiles
Custom Profile Development
Examples
ACMG Variant Pathogenicity Statement Example
ACMG Variant Pathogenicity Statement Example (with Evidence)
Custom Variant Pathogenicity Statement Example
Appendices
How to Participate
Development Process
SEPIO Modeling Framework
Design Decisions
Definition of ‘Variant Annotation’
Scope of Variant Knowledge Supported
Explicit Statement Semantics
Use of Propositions
Domain Entity Representation
Profile Authoring Mechanisms
Implementations
Variant Congruence
GA4GH Variant Annotation Specification
Appendices
Development Process
Edit on GitHub
Development Process