Unusual sex karyotype

Genomic sex inference also detects unusual sex karyotypes, which are defined as any sex karyotype other than XX or XY. However, sometimes the knowledge about the presence of such karyotype is important for interpretation of prioritised variants, for example if a hemizygous pathogenic variant is detected in a female with XO karyotype. In many other scenarios, it is expected that it won’t be relevant to the interpretation of the variants. Therefore to reduce the details of potential incidental findings, but to preserve the ability to access the information when relevant, the cases with unusual inferred sex karyotype are flagged with the UNUSUAL SEX KARYOTYPE flag.

The clinical scientist can contact Genomics England support for detailed information about the sex karyotype if it may be relevant for interpretation. Details for this can be found in the Variant Review SOP. Unusual sex karyotype inference, in the absence of sex discrepancy with the reported sex, does not trigger sex query in the pipeline.