Inconsistent NameChecker results for transcript-reference disagree
Created by: fennerm
I encountered some fairly unintuitive NameChecker behavior recently which initially lead me to generate an incorrect HGVS.
Background ALMS1 NM_015120.4 has a disagreement between the transcript and genomic reference sequences. In NC_000002.11 there are 8 GGA repeats at positions 2:73613032-73613070. In NM_015120.4 there are 9 repeats.
Expected result The recommended NM_015120.4 HGVS returned from the following two urls should be the same: https://www.mutalyzer.nl/name-checker?description=NC_000002.11%3Ag.73613050_73613070del https://www.mutalyzer.nl/name-checker?description=NM_015120.4%3Ac.54_74del
Actual result https://www.mutalyzer.nl/name-checker?description=NC_000002.11%3Ag.73613050_73613070del recommends NC_000002.11(ALMS1_v001):c.54_74del / NM_015120.4:c.54_74del. https://www.mutalyzer.nl/name-checker?description=NM_015120.4%3Ac.54_74del correctly identifies the reference disagree and recommends NM_015120.4:c.57_77del