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clingen-data-model / allele

Documentation for data model of ClinGen
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primary-transcript-region-type #142

Closed ronakypatel closed 9 years ago

ronakypatel commented 9 years ago

Not sure but is there term that can be used from primary-transcript-region-type value set for indels affecting upstream and downstream regions in addition to coding sequence?

NM_001126115.1:c.-3_13del16 http://www.ncbi.nlm.nih.gov/clinvar/variation/187254/

srynobio commented 9 years ago

You would only annotate the region where the change occurred, no where else on the transcript. A rough guess based on the ClinVar Variation Viewer looks like the change happens in a CDS, but you would need a couple of things to annotate the transcript type correctly:

Also keep in mind that for the first pass of transforming all the ClinVar data into the model, if ClinVar does not have an annotation for transcript-type you don't (initially) need to worry, it can be compulatally added later. This is the benefit of having the type in the model.

cbizon commented 9 years ago

The problem is that in this case, the deletion spans the start of the transcript. One could also imagine a frameshift(or non-frameshift) that spans an intron/exon boundary. I'm starting to wonder if we might have to change the cardinality of primary-transcript-region-type...

cbizon commented 9 years ago

Update the text about this