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  1. Jalview
  2. JAL-2041

clinical significance field not preserved in variant annotation from Ensembl

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Not A Bug
    • Affects Version/s: 2.10.0
    • Fix Version/s: 2.10.0
    • Labels:
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      Description

      The Ensembl variant view, for human at least, ought to faithfully preserve the 'clinical_significance' annotation for variants observed in a locus. Although the annotation appears to be present when exporting variant data from Jalview, its value is 'ARRAY(..)' - suggesting something along the data-retrieval chain is broken.

      1. select the Ensembl sequence source and import the example gene accession
      2. Export the features as GFF to text box. Variant features include something like:
      ENST00000479537 . sequence_variant 734 734 0.0 + . ID=sequence_variant:rs373128505;alleles=A,G;assembly_name=GRCh38;clinical_significance=ARRAY(0xf095520);consequence_type=3_prime_UTR_variant

      The ARRAY(0x...) looks like a server issue (raw array reference in perl?), but should be investigated.

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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