A Customized Next-Generation Sequencing-Based Panel to Identify Novel Genetic Variants in Dementing Disorders: A Pilot Study

Table 3

Results of the in silico analysis, along with evidence of pathogenicity.

Patient’s number	Gene	Variant	SIFT	PolyPhen-2 HDIV	MutationTaster	FATHMM	PROVEAN	CADD_phred	1000 Genomes (allele frequency)	Pathogenicity (ACMG guidelines) [21]	ClinVar
1	TREM2	c.482+2T>C							No data	5	Likely pathogenic
2	TREM2	c.482+2T>C							No data	5	Likely pathogenic
3	CHMP2B	c.C613T							No data	4	No data
4	CSF1R	c.G2239A	T	B	N	D	N	8.944	0.001	2	Likely benign
5	APP	c.G2137A							No data	5	Likely pathogenic
6	SERPINI1	c.G289A	T	B	N	D	N	0.024	0.002	1	Benign/likely benign​
7	GRN	c.C110G	T	D	N	T	N	20.4	No data	4	No data
8	APP	c.G1604A	T	D	D	T	N	28.5	No data	4	No data

Legend: A=harmful note; B=benign; D=deleterious; N=neutral; T=tolerated; ACMG=American College of Medical Genetics; 1=benign; 2=likely benign; 3=uncertain significance; 4=likely pathogenic; 5=pathogenic.