While the majority of CPG P/LP SNVs/InDels called by AutoGVP utilized ClinVar evidence, we identified 42 additional P/LP variants through AutoGVP’s modified InterVar classification, 18 P/LP SVs and one deep intronic NF1 variant previously classified as P/LP47, highlighting the importance of leveraging multiple approaches to characterize the full spectrum of disease-causing germline variation in pediatric cancers. Here, NF1 is linked to cancer.