Between-aminoacids deletion
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Thaís Córdova
Feb 7, 2025, 11:25:58 AMFeb 7
to HGVS Nomenclature
To HGVS,
I would like to ask if you could help me clarify the best way to properly name a variant I'm currently classifying in the CYP24A1 gene. The BAM file shows the deletion of three basepairs: NM_000782.5:c.428_430del - the c.428 corresponds to the second basepair of the triplet in p.143, which leads to a predicted in frame deletion of three base pairs and the creation of a single, new triplet. However, the software (and ClinVar) described this deletion as p.(Glu143del), which I do not believe to be the case. Also, I tried to simulate this variant in Alamut and it also returned the same result, but with the warning of non-HGVS compliant. Would it be more correct to describe it as a delins?
Thank you for your attention.
Very best wishes,
Thaís Córdova
CGC Genetics, Unilabs, Portugal
I would like to ask if you could help me clarify the best way to properly name a variant I'm currently classifying in the CYP24A1 gene. The BAM file shows the deletion of three basepairs: NM_000782.5:c.428_430del - the c.428 corresponds to the second basepair of the triplet in p.143, which leads to a predicted in frame deletion of three base pairs and the creation of a single, new triplet. However, the software (and ClinVar) described this deletion as p.(Glu143del), which I do not believe to be the case. Also, I tried to simulate this variant in Alamut and it also returned the same result, but with the warning of non-HGVS compliant. Would it be more correct to describe it as a delins?
Thank you for your attention.
Very best wishes,
Thaís Córdova
CGC Genetics, Unilabs, Portugal
Johan den Dunnen
Feb 7, 2025, 1:37:47 PMFeb 7
to HGVS Nomenclature
Dear Thais,
the predicted consequences of variant NC_000020.11:g.54172931_54172933del NM_000782.5:c.428_430del are r.(428_430del) p.(Glu143del). I am not sure why you think these predicted consequences are not correct. Also both VariantValidator and Mutalyzer give the same predicted consequences.
Best regards,
Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)
Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)
Op vrijdag 7 februari 2025 om 17:25:58 UTC+1 schreef Thaís Córdova:
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