Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1

Table 1 Evidence scoring system to select the pathogenic and benign ED variants that were used to define the usability and strength of the ACMG/AMP criteria

In favor of pathogenicity	In favor of neutrality
MAF < 0.0005% (all gnomAD v.2.1.1 non-cancer populations) AND: Somatic hotspot (≥ 10 tumors) OR Recurrent in PPAP families (≥ 3 families) and evidence of cosegregation with PPAP tumors^b in at least one family OR Variant affects a catalytic exonuclease site, and the residue change translates into a negative BLOSUM62 score OR Proofreading defective-associated mutational signatures SBS10, SBS14 and/or SBS20 identified in ≥ 2 tumors OR Variant is identified in a patient with a CMMRD-like phenotype in the absence of CMMRD (absence of germline biallelic MMR gene mutations) OR De novo germline variant in a patient with a tumor harboring SBS10, SBS14 and/or SBS20 mutational signatures	^aMAF ≥ 0.02% (all gnomAD v.2.1.1.non-cancer populations) OR ≥ 10 homozygotes (source gnomAD non-cancer individuals)

Abbreviations: CMMRD constitutional mismatch repair deficiency, gnomAD Genome Aggregation Database (https://gnomad.broadinstitute.org/), MAF minor allele frequency, MMR DNA mismatch repair, PPAP polymerase proofreading-associated polyposis
^aThe recurrent germline POLE ED pathogenic variant p.Leu424Val has a MAF in gnomAD of 0%, and the maximum number of gnomAD individuals harboring a known ED pathogenic variant is 1 (1 in ~ 230,000 alleles for POLD1 p.Asp316His).The established threshold in favor of neutrality implies the presence of the variant in ≥ 46 in 230,000 alleles
^bPPAP tumors include adenomatous polyposis, CRC, endometrial cancer, breast cancer, ovarian cancer, extracolonic GI cancer or brain cancer

ISSN: 1756-994X