TABLE 5.

Rare variants in AD-risk genes ABAC7 and SORL1 identified in this study.

Gene	ID patient	FH score	Nucleotide change	Protein change	Pathogenicity reported in ClinVar/HGMD	Possible role in EOAD	Frequency GnomAD (EU)1	P-value2
ABCA7	AD#009	0	c.2126_2132del AGCAGGG	p.Glu709Al afsTer86	Conflicting interpretations of pathogenicity; risk factor Uncertain significance (1) likely benign (1)/NR	Reported AD risk (De Roeck et al., 2019) risk factor	250/104264	0.18
	AD#052	3.5	c.2476G > A	p.Gly826Arg	NR/NR Prediction: likely pathogenic	Risk factor	95/126126	0.08
	AD#088	0	c.2629G > A	p.Ala877Thr	NR/NR Prediction: likely benign	Likely benign	1014/127604	0.41
	AD#006	0	c.3412A > C	p.Ser1138Arg	NR/NR Prediction: likely pathogenic	Risk factor	1/76428	0.01
	AD#009	0	c.3472 + 5G > C		NR/NR Prediction: likely benign	Possibly affecting splicing (Le Guennec et al., 2016) – Risk factor	2/112726	0.01
	AD#083	0	c.4343G > A	p.Gly1448Asp	NR/NR Prediction: likely benign	Likely benign	72/127544	0.07
	AD#007	0	c.4795G > A	p.Val1599Met	Likely benign/autism?	Likely benign	554/129150	0.28
	AD#028	3.5	c.5570 + 5G > C		Uncertain significance/Alzheimer disease?	Reported AD risk (De Roeck et al., 2019) risk factor	432/114436	0.05
	AD#099	0
SORL1	AD#094	3.5	c.133G > T	p.Asp45Tyr	NR/NR Prediction: likely pathogenic	Risk factor	4/39936	0.02
	AD#052	3.5	c.1805C > T	p.Ser602Leu	NR/Alzheimer disease?	Risk factor	NR	NA
	AD#096	0	c.3346A > G	p.Ile1116Val	Benign/Alzheimer disease, late-onset?	Likely benign	1065/129098	0.41
	AD#062	0	c.4077C > T	p.Cys1359=	Uncertain significance/NR	Risk factor	33/129196	0.03
	AD#097	0	c.5448T > C	p.Tyr1816=	Benign/NR	Likely benign	285/128866	0.18
	AD#088	0	c.6150A > G	p.Glu2050=	NR/NR Prediction: likely benign	Likely benign	1/113030	0.01

AD, Alzheimer disease, FH, family history, NA, not applicable, NR. Not reported. ¹Population allele frequencies referred to the European (non-Finnish) population reported on GnomAD v2.1.1, expressed as Allele count (Alt/total). ²P-value Fisher’s exact test, BH correction.