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clingen-data-model / allele

Documentation for data model of ClinGen
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Molecular consequence and functional consequence. #178

Closed srynobio closed 3 years ago

srynobio commented 8 years ago

@cbizon @larrybabb I was reviewing updates to the repository and noticed a few new pages:

 source/assertion/conceptual/molecular_consequence.md                         | 33 +++++++++++++++++++++++++++++++++
 source/assertion/implementation/value_set_list/molecular_consequence_type.md | 39 +++++++++++++++++++++++++++++++++++++++

I understand and see the value in creating this new list: value_set_list/molecular_consequence_type.md

However, the one question/issue I have is how this (source/assertion/conceptual/molecular_consequence.md) is being used here:

In addition, an allele can be stated to cause a loss of function. This allows, for instance, a stop-gain allele in the final codon of a CDS to be marked as not causing LOF.

I bring this up based on a past issue related to how ClinVar is using the same term, and how we don't want to conflate molecular consequence and functional consequence.