The impact of transcript alignment on variant interpretation
<p>The problematic gene list can be narrowed to 71 genes for hg79 and 15 genes for hg38 selecting the ones with clinical relevance based on coding transcripts (those with NM_* accession) and the ones associated with phenotypes in the Human Phenotype Ontology (HPO). Analyzing clinical data from allexes®, the reference data network connecting varvis® software setups, reveals that around 1.8% of clinical reports refer to genes with mapping gaps, impacting diagnostics across a significant number of diseases and patient records. Interestingly, these cases aren’t uniformly distributed but rather concentrated on a few transcripts, notably ALMS1 and SHANK3, representing about 45% of the affected cases in hg38 (Figure 2).</p>
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