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Clinical-Genomics-Lund / nextflow_wgs

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Test mimisbrunnr as a extra layer of clinical significance for CNVs #217

Open ViktorHy opened 3 weeks ago

ViktorHy commented 3 weeks ago

In a recent case a known duplication was estimated as being 1000 basepair shorter than previously called. This resulted in annotsv missmatch to dbvar and gnomad which caused the variant to loose 6 points for clinical significance, gained 2 points in allelefrequency and lost 3 points for gene conq.

This all indicates that it failed to match previously known variants in annotsv.

For details about samples contact me.

ViktorHy commented 3 weeks ago

Oh, and as I stated in title, one way to perhaps backup these cases in future could be to annotate svs with mimisbrunnr via svdb and adding the presence in mimisbrunnr to the clinical significance rank model category

ViktorHy commented 3 weeks ago

Open for other solutions as well. In this specific case I feel like the overlap of the dup to a very specific disease causing gene should be caught by more than previous clincial findings