Mutalyzer should normalise the same variant in different HGVS formats about mutalyzer2 HOT 3 OPEN

Original date: 2013/11/07
Original reporter: martijn

Dear Ken,

Thanks for the report. I assume you used the Position Converter.

This functionality is actually implemented in the Name Checker, see for example:

• NM_000059.3:c.670dup
• NM_000059.3:c.670_671insG

(NM references don't contain intronic sequences, so I modified your examples slightly so that the Name Checker can work with them.)

You're abolutely right that this is not implemented in the Position Converter and that is a bug. As it is now, the Position Converter does just that -- convert positions -- and is otherwise a pretty dumb tool.

We have plans to merge the two tools to have all the HGVS rules that are implemented in the Name Checker also available in the Position Converter, but this will take some time. In the meantime we sometimes patch the Position Converter to make it a bit smarter, but I don't think we will do that with this specific rule.

As for your problem, I would normally suggest to use the Name Checker on the output of the Position Converter. This won't work for intronic variants such as your example however.

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Original date: 2013/11/07
Original reporter: p DOT taschner AND lumc DOT nl

The Name Checker can check the original intronic changes after replacing NM_000059.3 by RefSeqGene NG_012772.1(BRCA2_v001).[[BR]]
NG_012772.1(BRCA2_v001):c.681+2dup and NG_012772.1(BRCA2_v001):c.681+1_681+2insT will result in the recommended description:[[BR]]
NG_012772.1(BRCA2_v001):c.681+2dup

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Original date: 2013/11/07
Original reporter: martijn

That's a good point by Peter, and I can add that we plan to implement RefSeqGene (NG) mappings in the Position Converter (currently it only has NM mappings).

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