Hi @Christophe,
Thank you for your report! @ajfriedman18 is correct that our VCFs have 46 fields in the VEP header and 48 fields in the annotation: both extra annotation fields are simply missing values. This was a bug in our VCF export code and the annotation should have matched the VCF header with 46 fields. We will be fixing this in our v4.1 release.
Apologies for the confusion/frustration this has caused!
Best,
Mike