2.25. Variant coding impact for duplications of 5' splice sites in genes on positive strand may be missed
Duplications located on the 5' intron-exon boundary of a coding region for a gene on the positive strand are reported as insertions in the intron rather than a duplication within the exon. This is due to the left-alignment of insertions relative to the reference sequence in both Workbenches, as described in the manual section Gap placement.
A duplication at a 5' intron-exon junction must be present in a gene on the positive strand for this issue to affect results.
Genes on the negative strand are not affected by this issue.
An affected variant would not be reported as having a coding impact, when it should be reported as have a coding impact, when using the "Add Information about Amino Acid Change" tool in the Biomedical Genomics Workbench or the "Amino Acid Change" tool in the CLC Genomics Workbench.
This problem is affected to arise infrequently, due to the nature of the variants affected.
- Biomedical Genomics Workbench 2.1 through 5.0
- CLC Genomics Workbench 5 through 11.0
- CLC Genomics Server 4.0 through 10.0
This issue was addressed in Biomedical Genomics Workbench 5.0.1, CLC Genomics Workbench 11.0.1 and CLC Genomics Server 10.0.1.