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3' aligned spice junction g. insertions are not aligned upon c. conversion when strand is negative #809

@crutching

Description

@crutching

Imagine a variant in hg19 space:

chromosome = '21'
position = 36252851
ref = 'T'
alt = 'TAGG'

This is ambiguous with:

chromosome = '21'
position = 36252852
ref = 'A'
alt = 'AGGA'

According to the 3' rule, either of these would result in:
NC_000021.8:g.36252852_36252853insGGA

Translation to c. becomes:
NM_001754.5:c.508+1_508+2insTCC

We believe the actual change here should be the following, based on 3' realignment of the coding sequence, oriented on the negative strand:
NM_001754.5:c.508+2_508+3insCCT

Setting a g. nomenclature without realignment (36252851_36252852insAGG) yields the correct coding nomenclature.

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