Probably benign. Predicted to be damaging by Polyphen 2 and other damaging variants cause Alagille syndrome, but this variant is not rare enough and has been seen in a healthy PGP participant.
This variant is predicted to be damaging by Polyphen 2, but has been seen heterozygously in 2 out of 23 PGP + public genomes. Other variants in NOTCH2 are reported to cause Alagille syndrome in a dominant manner. The presence of this gene in a healthy PGP participant and the relatively common allele frequency (2-4%) contradicts this variant as having a significant high penetrance pathogenic effect, and so we tentatively evaluate it as benign.