Table 2.

List of rare and novel GRAMD1B variants identified in MS cases. For each variant, the frequency in familial (AF familial multiple sclerosis, n = 92) and sporadic multiple sclerosis (AF sporadic multiple sclerosis, n = 192) cases, in two cohorts of Italian healthy controls (the first using Sanger sequencing (AF HC cohort 1, n = 296) and the second using next-generation sequencing data from the Italian Reference Genome v1 (AF HC cohort 2, n = 1099)). Additional ions are shown.

POS	11:123464786	11:123476158	11:123484303	11:123484370	11:123485455
SNP	rs118067934	rs140366389	rs755488531	rs769527838	.
REF	G	C	G	T	T
ALT	A	G	A	G	C
AF fMS (n = 91)	0.0205	0.005	0.005	0.006	0.005
AF sMS (n = 192)	0.0104	0.005	0	0	0
AF HC cohort 1 (n = 296)	0.172	0.009	0	0	0
AF HC cohort 2 (n = 1096)	0.024	0.001	0	0	0
IMPACT	LOW	MODERATE	MODERATE	LOW	MODERATE
CODON	c.256-4G > A	c.866C > G	c.1735G > A	c.1798 + 4T > G	c.1801T > C
AA change	.	p.Ser289Cys	p.Val579Met	.	p.Ser601Pro
GERP++ RS	.	4.83	5.52	.	4.72
Polyphen2 HDIV	.	0.986 (D)	0.978 (D)	.	1.0 (D)
SIFT	.	0.005(D)	0.274(T)	.	0.006 (D)
CADD PHRED Score	8.347	24.5	24.8	10.66	24.0

CHR: chromosome; POS: position according to hg19 database; SNP: SNP name if available; REF: reference allele; ALT: alternative allele; IMPACT: predicted impact of the genetic variant on protein function according to SnpEff; CODON: codon change; AA change: amino acid change; GERP++ RS: GERP score according to dbNSFP; Polyphen2 HDIV score according to dbNSFP; SIFT score according to dbNSFP; CADD (combined annotation-dependent depletion) PHRED score.