incomplete_transcript_variant [SO_0002075]

A sequence variant that intersects an incompletely annotated transcript. This term is to map to the ANNOVAR term ‘ncRNA’ http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) ‘variant overlaps a transcript without coding annotation in the gene definition’. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation. It is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems.

Open incomplete_transcript_variant in VFB

VFB Term Json

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            "iri": "http://purl.obolibrary.org/obo/SO_0002075",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "SO_0002075",
            "label": "incomplete_transcript_variant"
        },
        "description": [
            "A sequence variant that intersects an incompletely annotated transcript."
        ],
        "comment": [
            "This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation.\n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/SO_0001576",
            "types": [
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                "Class"
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            "short_form": "SO_0001576",
            "label": "transcript_variant"
        }
    ],
    "relationships": [],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [
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            "synonym": {
                "scope": "has_exact_synonym",
                "label": "incomplete transcript variant",
                "type": ""
            },
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                "PubMed": "",
                "DOI": ""
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}