The varvis® team often receives questions regarding the HGVS notation of variants that are challenging to annotate because they are affected by alignment (mapping) 'gaps' between RefSeq transcripts and reference genomes.
These gaps are one of the main reasons why bioinformatics tools may disagree with each other on predicted cDNA change, predicted protein change, or even exon count.
This repository provides lists RefSeq transcripts with mapping issues for specific transcript<->reference alignment versions. They allow to quickly check whether tools may disagree about a variant because of this issue, as a first step for troubleshooting.
If you find any issue regarding the transcript meta-data we provide, please report it.
More details on mapping gaps are given in the talk "Mind the gaps: Impact of transcript alignment on variant interpretation" from the varvis® corporate satellite at ESHG 2022.