Thanks for writing this, it’s not something I’d looked at before but I read some of the Promethease sample reports because you got me interested.
There does seem to be some weird normalisation going on when calculating magnitude. For instance this gene gives a score of 0 for (C;C) and bad magnitude of 2.7 and 3.1 for (C;G) and (G;G) respectively. So if you have (C;C) and you filter by magnitude 2 you miss out on the fact that you have an advantageous genotype.
This isn’t a problem if (C;C) is extremely common but actually it’s no more common than (C;G) (except for people of African descent), so the act of filtering prevents you from realising that you missed a 50:50ish chance of getting a disadvantageous genotype.
So probably to work this out properly you can’t filter by magnitude and you’d have to open up every genoptye details to check for what you’ve avoided getting hit by. You could only really work out how well you’ve done compared to other people where the data includes frequency so you could see just how lucky/unlucky you got for a particular gene.
Not all of the genotypes have this issue—for instance this gene seems to be more sensibly normalised. If they were all done like this then I’d be much happier with the system.