wrong annotation

[Thiel, Christian]

Dear Ladies and Gentlemen,

 

using your software, we came up with a wrong annotation of the Variant: Chr11:111711376A>T (NC_000011.9:g.111711376A>T)

Your position converter came up with the following info:

 

Chromosomal variant

NC_000011.9:g.111711376A>T

Found transcripts in variant region

ALG9      :      NM_001077691.1:c.660+2T>A

                 NM_001077692.1:c.660+2T>A

                 NM_001077690.1:c.1174+2T>A

                 NM_024740.2:c.1174+2T>A

 

For the transcript number NM_024740.2 the correct annotation would be c.1173+2T>A not c.1174+2T>A

The corresponding ClinVar entry is:

VCV000162619.3 - ClinVar - NCBI (nih.gov)

 

Could you please clarify this issue.

 

Mit freundlichen Grüßen,

 

Christian Thiel

 

Prof. Dr. med. Christian T. Thiel, MBA

Oberarzt

 

Humangenetisches Institut

Friedrich-Alexander-Universität Erlangen-Nürnberg

Schwabachanlage 10

91054 Erlangen

 

Phone: +49-9131-85-44637

FAX: +49-9131-85-23232

email: Christi...@uk-erlangen.de

 

 

[Mihai Lefter]

Dear Christian Thiel,

Thank you for using Mutalyzer.

The issue that you mention is related to the annotation used by Mutalyzer 2 (for the exon locations of "NM_024740.2" in "NC_000011.9"), which is old (but still provided by the NCBI in GenBank format as the most recent one [1]).

You can check Mutalyzer 3, which uses a more recent annotation source that leads to the description that you also mention (see the equivalent descriptions in [2]).

Please have a look also at section 7 from [3] for more details regarding annotation changes not reflected in reference ID updates.

Best regards,
Mihai

[1]: https://www.ncbi.nlm.nih.gov/nuccore/NC_000011.9

[2]: https://v3.mutalyzer.nl/namechecker/NC_000011.9:g.111711376A%3ET
[3]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479679/#__sec26title