GA4GH Variant Annotation Specification

The Variant Annotation Specification (VA-Spec) is a standard developed by the Global Alliance for Genomics and Health (GA4GH) to facilitate sharing of biological and clinical knowledge about genetic variation. It consists of a foundational domain-agnostic VA Core Model, Profiles derived from this core model that provide schema for specific types of variant knowledge, and a Python Reference Implementation. Documentation on this site describes the motivation, content, utility, and implementation guidance for the specification.

Section	Description
Introduction	An entry point for understanding the VA-Spec, introducing its motivation, components, use cases, and development approach.
Modeling Foundations	An overview of the modeling design patterns and principles that underpin the VA-Spec.
VA Core Model	Detailed descriptions of the classes and attributes in the domain-agnostic VA Core Model, and how to use them.
VA Profiles	Detailed descriptions of the domain-specific Statement, Evidence Line, Proposition, and Study Result Profiles included in the VA-Spec.
Reference Implementation	Information about code libraries provided to facilitate implementation of the VA-Spec.
Developer Guide	Practical, developer-focused support for authoring and implementing VA Profiles in data systems.
Examples	A set of annotated data examples and scenarios that demonstrate use of VA Models.
Appendices	A collection of pages with additional information on various aspects of the VA-Spec.

If you have questions or feedback, please reach out to the VA Team through our mailing list, or in our issue tracker.

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Full Site Map:

• 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