Variants on chrY are annotated with genes located on chrX (non-PAR region)

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

https://www.ensembl.org/vep

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Variants on chrY are annotated with genes located on chrX (non-PAR region) #1760

Closed bartcharbon closed 2 months ago

bartcharbon commented 2 months ago

Describe the issue

We have variants on the chrY contig that get annotated with the "NLGN4X" gene, while this gene is located on chrX. This gene is not in the PAR regions. A similar gene "NLGN4Y" is located in the region of our variants (chrY:14,522,573-14,845,654).

System

VEP version: 111
VEP Cache version: homo_sapiens_refseq_vep_111_GRCh38

bartcharbon commented 2 months ago

Further inspection showed that the reported variant is a translocation event from X