Errors while checking batch type job for HGVS name checker

[Mayher Patel]

Dear Mutalyzer,

I am trying to check a list of variants to make sure the HGVS nomenclature is correct. At first I listed "NM_" identifiers for the variants but then for the intronic variants I changed them to "NC_" identifiers. Before publishing the data from these variants, the journal Genetics in Medicine would like us to ensure there are no errors or warnings that appear in the Name Checker tool.

Attached is the file generated by the database/algorithm for checking the HGVS names for the variants included in our manuscript. There are a few warnings such as "(GenRecord): Mutation near splice site in gene COCH transcript 001.|(GenRecord): Mutation near splice site in gene COCH transcript 002.|(GenRecord): Mutation near splice site in gene COCH transcript 003.|(GenRecord): Mutation near splice site in gene COCH transcript 004.|(GenRecord): Mutation near splice site in gene COCH transcript 006.|(GenRecord): Mutation near splice site in gene COCH transcript 007." 

Does this mean the HGVS nomenclature is incorrect and how can we pass the checker without any warnings/errors? These errors/warnings only appear in intronic variants.

Thank you for the clarification. 

Best,

Mayher

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Mayher Patel (he/him/his) | Research Associate

105 Broadway, Cambridge, MA 02142

Email: may...@broadinstitute.org

[Mihai Lefter]

Dear Mayher,

Thank you for using Mutalyzer.

Warnings are usually given to inform users that care needs to be taken when

interpreting the effect of a variant. In your case, the warnings about variant

in splice sites may indicate possible mis-predictions of the protein change.

However, those descriptions are correct.

Best regards,

Mihai

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