[ensembl-dev] Dev Digest, Vol 35, Issue 1

[Ziv Lang]

I've sent unsubscription request a few  times, yet I keep getting these
emails.

בתאריך יום ו׳, 21 בינו׳ 2022, 16:26, מאת Syed Hossain ‏<snhossain at ebi.ac.uk
>:

> On 2022-01-20 18:00, dev-request at ensembl.org wrote:
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> > Today's Topics:
> >
> >    1. Change in consequence and HGVSp between VEP v99 and v100
> >       (Wallace Ko)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 20 Jan 2022 13:02:47 +0800
> > From: Wallace Ko <myko at l3-bioinfo.com>
> > To: Ensembl developers list <dev at ensembl.org>
> > Subject: [ensembl-dev] Change in consequence and HGVSp between VEP v99
> >       and v100
> > Message-ID:
> >       <
> CAMsJki0yY4PZG7sSYiNx-SkifAXrVcFsURgMKsZ3Q4Gz7ta_xg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello Ensembl Team,
> >
> > During re-evaluation of some old samples, we found that VEP v99 and
> > v100
> > give the same HGVSc, but different annotation, including consequence
> > and
> > HGVSp, e.g.:
> >
> >    1. HGVSc: NM_001034954.1:c.182T>C
> >       - v99:
> >          - HGVSp: NP_001030126.1:p.Pro61=
> >          - Consequence: synonymous_variant
> >       - v100:
> >          - HGVSp: NP_001030126.1:p.Leu61Pro
> >          - Consequence: missense_variant
> >       2. HGVSc: NM_000283.3:c.928-9_940dup
> >    - v99 HGVSp:  NP_000274.2:p.Tyr314CysfsTer50
> >       - v100 HGVSp:  -
> >    3. HGVSc: NM_001040108.1:c.4243-36_4243-1dup
> >       - v99 HGVSp:
> >
> > NP_001035197.1:p.Gln1414_Ile1415insHisIleAlaAsnTerSerTyrSerPhePheProTer
> >       - v100 HGVSp:  NP_001035197.1:p.Gln1414_Ile1415insHisIleAlaAsnTer
> >
> > I tried using offline VEP v100 with v99 cache and vice versa. VEP v100
> > produces the new results regardless of the cache being used. So it
> > should
> > be due to code change instead of data update.
> >
> > The change is sort of significant but there seem no relevant details in
> > the
> > release descriptions (
> > https://github.com/Ensembl/ensembl-vep/releases?q=release%2F100) or the
> > mail list about the change.
> >
> > I wonder what causes such changes and if there is a scope or pattern on
> > the
> > changes. Otherwise, we may need to re-analyze all results from VEP v99
> > or
> > older.
> >
> > Thank you.
> >
> > Regards,
> > Wallace Ko
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> > End of Dev Digest, Vol 35, Issue 1
> > **********************************
>
> Hello Wallace,
>
> Thank you for reporting this issue. But, unfortunately, we were unable
> to reproduce it.
>
> For our case VEP v99 is also giving the same output as what you get for
> VEP v100 (i.e - HGVSc: NM_001034954.1:c.182T>C --> HGVSp:
> NP_001030126.1:p.Leu61Pro).
>
> Can you kindly share the full command you are using and (if possible)
> the input files.
>
> Best regards,
> Nakib
>
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