Relative Allele

Definition and Information Model

Draft

May change significantly in future releases. See 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.
type		string	1..1	MUST be “RelativeAllele”
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
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.

Inherits: Molecular Variation

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.