variant allele [GENO_0000002]

An allele that varies in it sequence from what is considered the reference or canonical sequence at that location. Note that what is considered the ‘reference’ vs. ‘variant’ sequence at a given locus may be context-dependent - so being ‘variant’ is more a role played in a particular situation. A ‘variant allele’ contains a ‘sequence alteration’, or is itself a ‘sequence alteration’, that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a ‘reference’ vs the ‘variant’ is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being ‘variant’ is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. A variant allele can be variant along its entire extent, in which case it is considered a ‘sequence alteration’, or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence.

Open variant allele in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000002",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000002",
            "label": "variant allele"
        },
        "description": [
            "An allele that varies in it sequence from what is considered the reference or canonical sequence at that location."
        ],
        "comment": [
            "Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference.  So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another.\n\nA variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part.  And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000512",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000512",
            "label": "allele"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/GENO_0000683",
                "label": "varies_with",
                "type": "varies_with"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/GENO_0000036",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "GENO_0000036",
                "label": "reference allele"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}