[ensembl-dev] Change in consequence and HGVSp between VEP v99 and v100

[Syed Hossain]

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

On 2022-01-20 13:02:47 +0800, Wallace Ko wrote:
> 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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