[ensembl-dev] MANE transcript for GNAS

[Jamie Allen]

Hi Wallace,

The MANE transcript in this case does not overlap that particular variant, though other transcripts of this gene do (such as ENST00000371075.7, which is in the MANE clinical plus set).

rs1800900 is at chr20: 58,840,055 and the MANE transcript you mention (ENST00000371085.8) is located at chr20: 58,891,421-58,911,192

So no, the VEP cache is correct in this case - hope this clears it up, but please reach out if you have any other questions.

Cheers,
Jamie.


> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 19 Jan 2024 12:29:06 +0800
> From: Wallace Ko <myko at l3-bioinfo.com>
> To: Ensembl developers list <dev at ensembl.org>
> Subject: [ensembl-dev] MANE Select/Canonical transcript not found in
> 	VEP result
> Message-ID:
> 	<CA+DTqFcm-0SdEMrXv2RONzN4x_pRxJqhez7VUzJ_L29SzSobaw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Ensembl Development Team,
> 
> In Ensembl website for the gene GNAS (
> https://ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000087460;r=20:58839718-58911192),
> the transcript table show the record ENST00000371085.8 with MANE Select
> flag.
> 
> However, in VEP result (from version 111 with cache) or web (
> https://www.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=WAAIGImXnul0ZVhG)
> for the variant rs1800900, the result for ENST00000371085 cannot be found.
> Would there be something wrong with VEP v111 or the cache itself?
> 
> Regards,
> Wallace Ko
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