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Confusing HGVS notation for RNA changes

Hello all,

I'm trying to clean up variants notations in an in-house database, and stumbled upon a case that has the following RNA variant pattern:

r.[duplication; insertion , duplication] + [0]

I'm unable to understand what the [0] could possible mean in this context. [n] is usually used to annotate repeats, in much the same way as {n} is used in regular expressions. For example, c.35TA[3] would mean a TA di-nucleotide repeat occurring thrice (so, a 6 base insert) at position 35 in the cDNA sequence. But what could + [0] mean here?

I'd appreciate any help!

hgvs rna
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written by Ram Ram

Could you post the exact variant for clarification? The only time I see [0] mentioned in the HGVS standards is from: here http://www.hgvs.org/mutnomen/standards.html

  • 0 (zero) = indicates no product / nothing
    • c.0 = no DNA from allele detected, e.g. c.[76A>C];[0] for a variant in a X-linked gene in a male
    • r.0 = no RNA from allele detected, e.g. from a promoter variant or deletion
    • p.0 = no protein from allele detected, e.g. from a variant in the translation initiation codon

Which would imply no RNA from this allele, but I have no idea what the + sign would mean then.

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updated by Ram Ram • written by dandan dandan

I'm not sure if that will help. The exact mutation is a novel variant, found in our clinical lab. I was able to parse the duplication and insertion parts perfectly, and they were in exactly the same format as insertions/duplications are in today.

The sequencing expert labeled it that way a few years back, and the person has since moved on to a different workplace. This person did mention that the labeling conformed to "current" conventions, so is there any chance we could be dealing with obsolete conventions from around 7 years ago?

If that's the case, any place I could check for the history of these conventions?

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written by Ram Ram

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