Choosing against one condition can raise the risk of another
The genes are not sorted by disease. Pushing one number down pushes others somewhere, and mostly nobody knows where.
One stretch of DNA can affect many things at once. So when you rank embryos on one score, you are also, silently, ranking them on others.
There is exactly one published example that gives both a relative and an absolute figure, and it is the one to hold on to. From the NEJM paper: if an embryo is selected on the basis of the polygenic score for educational attainment, the risk of bipolar disorder is increased by 16% from an absolute risk of 1.0% to 1.16%.
A second example is published without a number, and it should be read that way. The Cell paper states: while IQ is negatively correlated with most psychiatric disorders, it is genetically positively correlated with autism and anorexia. Therefore, selecting an embryo on the basis of higher predicted IQ will increase the risk for autism or anorexia in the offspring.
Those authors give no magnitude for it, so this guide gives none either. It tells you the direction, not the size.
The schizophrenia modelling paper does publish sizes for this effect, but only as relative increases. It publishes no matching absolute figures. Since this guide does not print a relative figure without the absolute one beside it, those numbers are left out, and the honest statement is this: the size of the trade-off has been modelled but the absolute risk increase it implies has not been published.
Two more things follow, and both come from the researchers rather than from critics.
You cannot simply select against the side effect as well: the risk of bipolar disorder would not be fully mitigated, because the polygenic score for bipolar disorder is not yet as predictive as that for educational attainment. Moreover, since selection in favor of one trait and against the other means that the embryo with the highest polygenic score for educational attainment cannot necessarily be selected, addressing the risks of pleiotropy would reduce the expected gain from ESPS.
And you cannot check the whole list, because there is no whole list: The vast majority of relationships between genetic variants and traits are not yet known.
The European genetics society points out why patients rarely hear about this: individual variants may increase the risk for one trait, while simultaneously reducing the risk of another. This complexity is often not obvious to individuals who request information about their future risk through PRS, because they are only informed about the risk for a specific trait that they have sought advice for.
"Does your report show me the conditions that move in the wrong direction, or only the ones I asked about?"
"Give me any increase as an absolute number too."