Relative Allele

Definition and Information Model

Warning

This data class is at a draft maturity level and may change significantly in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

An Allele defined on a mapped location relative to a base location. Often used to describe intronic variants.

GA4GH Digest

Prefix	Inherent
RA	[‘baseState’, ‘mappedState’, ‘relativeLocation’, ‘type’]

Information Model

Some RelativeAllele attributes are inherited from Variation.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
digest		string	0..1	A sha512t24u digest created using the VRS Computed Identifier algorithm.
expressions	⋮	Expression	0..m
type		string	1..1	MUST be “RelativeAllele”
mappedState		Sequence Expression	1..1	The state of the RelativeAllele as expressed on the mapped sequence. This will differ from the base state when mapping to a reverse complement sequence, commonly observed when representing the state on transcripts mapped to the “negative strand” of a chromosome.
baseState		Sequence Expression	1..1	The state of the RelativeAllele as expressed on the base sequence.
relativeLocation		Relative Sequence Location | iriReference	1..1	The relative location at which the baseState and mappedState are expressed.

Example

There are several Splice-Adjacent HGVS Variant Examples with more details. Below is an example of a splice acceptor downstream relative allele.

{
  "type": "RelativeAllele",
  "relativeLocation": {
    "baseSequenceLocation": {
      "type": "SequenceLocation",
      "sequenceReference": {
        "type": "SequenceReference",
        "id": "NC_000010.11",
        "refgetAccession": "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB"
      },
      "start": 95387120,
      "end": 95387121
    },
    "mappedSequenceLocation": {
      "sequenceReference": {
        "type": "SequenceReference",
        "id": "NM_001034954.3",
        "refgetAccession": "SQ.SDt4gIJa8ChOmuI3te-3gpbJExmt1dHX"
      },
      "anchor": 1543,
      "anchorOrientation": "right",
      "offsetStart": -2837,
      "offsetEnd": -2836
    }
  },
  "mappedState": {
    "type": "LiteralSequenceExpression",
    "sequence": "G"
  },
  "baseState": {
    "type": "LiteralSequenceExpression",
    "sequence": "C"
  }
}

Implementation Guidance

Normalization

The RelativeAllele also includes conventions for variant normalization (see Relative Allele Normalization) that allows for compact and uniform representation of relative allele variants.