errors
Suma Shankar
Hi,
I am receiving errors when I upload these variants
NM_001077394.1:c.779A>G
NM_001077394.1:c.329A>G
NM_001077394.1:c.619C>T
NM_001077394.1:c.521dup
https://mutalyzer.nl/batch-job-result/batch-job-e2f0fe13-dd11-49c2-8d4c-2739549d5e3b.txt
On NCBI the Homo sapiens diphthamide biosynthesis 5 (DPH5), transcript variant 1, mRNA
NCBI Reference Sequence: NM_001077394.1
This sequence has been updated. See current version.
https://www.ncbi.nlm.nih.gov/nuccore/NM_001077394
has been replaced with NCBI Reference Sequence: NM_001077394.2
https://variantvalidator.org/service/validate/
However, if I use the NCBI Reference Sequence: NM_001077394.2 version it doesn’t work.’
Would much appreciate any help and suggestion on how to get an updated vesrion and an excel output for submission to Genetics in Medicine.
Thanks,
Suma
Suma Shankar MD., PhD
Director, Precision Genomics
Children’s Miracle Network Endowed Chair in Pediatric Genetics
Associate Professor, Division of Genomic Medicine
Departments of Pediatrics & Ophthalmology
University of California Davis, MIND Institute
2825, 50th Street, Sacramento, CA 95817
Academic Office: 916 703 0235
Clinic: 916 703 0300
Fax: 916 703 0203
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J.F.J. Laros
Thank you for using Mutalyzer.
At the moment it is unclear to me which errors you are referring to. In the
batch job result, no errors are reported and both the old [1] as well as the
new [2] reference sequences seem to work fine.
Could you give an example of what goes wrong in your opinion?
With kind regards,
Jeroen.
References:
[1] https://mutalyzer.nl/name-checker?description=NM_001077394.1%3Ac.779A%3EG
[2] https://mutalyzer.nl/name-checker?description=NM_001077394.2%3Ac.779A%3EG
On Tue, Nov 02, 2021 at 06:20:56AM +0000, 'Suma Shankar' via Mutalyzer wrote:
> Hi,
>
> I am receiving errors when I upload these variants
>
> NM_001077394.1:c.779A>G
> NM_001077394.1:c.329A>G
> NM_001077394.1:c.619C>T
> NM_001077394.1:c.521dup
>
> https://mutalyzer.nl/batch-job-result/batch-job-e2f0fe13-dd11-49c2-8d4c-2739549d5e3b.txt
>
> On NCBI the Homo sapiens diphthamide biosynthesis 5 (DPH5), transcript variant 1, mRNA
>
> https://www.ncbi.nlm.nih.gov/nuccore/NM_001077394
>
> has been replaced with NCBI Reference Sequence: NM_001077394.2
>
> https://variantvalidator.org/service/validate/
>
> However, if I use the NCBI Reference Sequence: NM_001077394.2 version it doesn’t work.’
>
> Would much appreciate any help and suggestion on how to get an updated vesrion and an excel output for submission to Genetics in Medicine.
>
>
> Thanks,
>
> Suma
>
> Suma Shankar MD., PhD
> Director, Precision Genomics
> Children’s Miracle Network Endowed Chair in Pediatric Genetics
> Associate Professor, Division of Genomic Medicine
> Departments of Pediatrics & Ophthalmology
> University of California Davis, MIND Institute
> 2825, 50th Street, Sacramento, CA 95817
> Academic Office: 916 703 0235
> Clinic: 916 703 0300
> Fax: 916 703 0203
>
> CONFIDENTIALITY NOTICE: This email message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential, proprietary, and/or privileged information protected by law. If you are not the intended recipient, you may not use, copy, or distribute this email message or its attachments. If you believe you have received this email message in error, please contact the sender by reply email and destroy all copies of the original message.
>
>
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--
Jeroen F.J. Laros - J.F.J...@lumc.nl
Suma Shankar
Got it- thanks for your reply!
Much appreciate your help.
Thanks,
Suma
CONFIDENTIALITY NOTICE: This email message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential, proprietary, and/or privileged information protected by law. If you are not the intended recipient, you may not use, copy, or distribute this email message or its attachments. If you believe you have received this email message in error, please contact the sender by reply email and destroy all copies of the original message.
From:
J.F.J. Laros <J.F.J...@lumc.nl>
Date: Tuesday, November 2, 2021 at 8:05 AM
To: Suma Shankar <spsh...@ucdavis.edu>
Cc: muta...@googlegroups.com <muta...@googlegroups.com>
Subject: Re: [mutalyzer] errors
Dear Suma Shankar,
Thank you for using Mutalyzer.
At the moment it is unclear to me which errors you are referring to. In the
batch job result, no errors are reported and both the old [1] as well as the
new [2] reference sequences seem to work fine.
Could you give an example of what goes wrong in your opinion?
With kind regards,
Jeroen.
References:
[1]
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmutalyzer.nl%2Fname-checker%3Fdescription%3DNM_001077394.1%253Ac.779A%253EG&data=04%7C01%7Cspshankar%40ucdavis.edu%7Ce67fd6aeaeae44eba65708d99e123221%7Ca8046f6466c04f009046c8daf92ff62b%7C0%7C1%7C637714623255411123%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=rjZLK9IbuyZ8hVeaFUe0t20wqJ3ngAcqsKVKoMXiUE0%3D&reserved=0
[2]
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmutalyzer.nl%2Fname-checker%3Fdescription%3DNM_001077394.2%253Ac.779A%253EG&data=04%7C01%7Cspshankar%40ucdavis.edu%7Ce67fd6aeaeae44eba65708d99e123221%7Ca8046f6466c04f009046c8daf92ff62b%7C0%7C1%7C637714623255411123%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=e8CfvcF04gpc8Im%2BAFddeUTPFsGpyiTmUiaU8qt5AkE%3D&reserved=0
On Tue, Nov 02, 2021 at 06:20:56AM +0000, 'Suma Shankar' via Mutalyzer wrote:
> Hi,
>
> I am receiving errors when I upload these variants
>
> NM_001077394.1:c.779A>G
> NM_001077394.1:c.329A>G
> NM_001077394.1:c.619C>T
> NM_001077394.1:c.521dup
>
>
> On NCBI the Homo sapiens diphthamide biosynthesis 5 (DPH5), transcript variant 1, mRNA
> This sequence has been updated. See current version.
>
>
> has been replaced with NCBI Reference Sequence: NM_001077394.2
>
>
> However, if I use the NCBI Reference Sequence: NM_001077394.2 version it doesn’t work.’
>
> Would much appreciate any help and suggestion on how to get an updated vesrion and an excel output for submission to Genetics in Medicine.
>
>
> Thanks,
>
> Suma
>
> Suma Shankar MD., PhD
> Director, Precision Genomics
> Children’s Miracle Network Endowed Chair in Pediatric Genetics
> Associate Professor, Division of Genomic Medicine
> Departments of Pediatrics & Ophthalmology
> University of California Davis, MIND Institute
> 2825, 50th Street, Sacramento, CA 95817
> Academic Office: 916 703 0235
> Clinic: 916 703 0300
> Fax: 916 703 0203
>
> CONFIDENTIALITY NOTICE: This email message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential, proprietary, and/or privileged information protected by law. If you are not the intended recipient, you may
not use, copy, or distribute this email message or its attachments. If you believe you have received this email message in error, please contact the sender by reply email and destroy all copies of the original message.
>
>
> **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error,
be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.
>
> --
> You received this message because you are subscribed to the Google Groups "Mutalyzer" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to mutalyzer+...@googlegroups.com.