John Gill Commentary Genesis 46:26

"All the souls that came with Jacob into Egypt, that came out of his loins, besides Jacob`s sons` wives, all the souls were threescore and six;" — Genesis 46:26 (ASV)

All the souls that came with Jacob into Egypt These are in parcels before mentioned, but here they are brought to a sum total; and by this phrase are excluded those that died before, as Er and Onan, and those that were in Egypt before, as Joseph and his two sons; and I should think also all that were born in Egypt afterwards, even while Jacob was living.

Those reckoned are only such, which came out of his loins : such as were his seed and offspring. This is observed for the sake of what follows, and to exclude them: besides Jacob's sons' wives ; these do not come into the account, because they did not spring from him.

all the souls [were] threescore and six ; thirty two of Leah's, leaving out Er and Onan, sixteen of Zilpah's, fourteen of Rachel's, and seven of Bilhah's, make sixty nine; take out of them Joseph and his two sons, who were in Egypt before, and you have the exact number of sixty six.