Authors present the results of a study aimed to detect in nsOFC cases the association with variants in five genes previously identified by GWAS.
Information about the cases is scares: it is not clear if cases were part of parental trios or isolated. Information about sex, cleft types, percentage of each populations is missing.
In Results Authors should make clear which are the characteristics of what they considered “variant of interest”. Moreover, it should be make clear which variants were inherited and which were de-novo.
The Discussion should provide comment on the role of inherited variants vs de-novo variants, according to the obtained results.
In the Introduction Authors must provide some details about the genes identified by GWAS od WES in nsOFC cases, and explain the reason why among them they chose to study only five, namely SHH, RORA, MRPL53, ACVR1, and GDF11.
Page 5 line 43. Better to say “insufficient intake of folates”, as “folates” includes both natural and synthetic (folic acid) folates.
Page 6 line 10: it is not clear what the 1141 samples are: where cases recruited as trios, so the total number of samples includes also parents, as parents are mentioned at page 8 lines 12-16?
Page 6 line 36: please specify the kit that had been used.
Page 6, lines 40-43: please include reference of the method.
Page 6 lines 52-53: better to include information on primer pairs as supplemental material.
Page 7 line 5-7: add reference for PCR amplification or details (which volume, which reaction mix?).
Figure 1 does not provide any relevant information to the paper, and could be omitted.
Figure 2 is almost impossible to read. Maybe resolution could be improved and figure provided as supplemental data.
Table at page 23 seems with no legend.
OFC acronym should be used instead of CPO/CL/P

Authors successfully replied to comments and modified their manuscript accordingly
Just one last note: page 5 line 43: “intake of” is duplicated. Please correct.

Authors successfully corrected a minor typo.