Spectrum of genomic variations in Indian patients with progressive familial intrahepatic cholestasis

BMC Gastroenterology

Table 4 ‘Benign’ or ‘likely benign’ non-synonymous genomic variations identified in Indian patients with PFIC syndrome

Gene	Nucleotide change	AA change	Inclusion in databases^a			Allele frequency reported in ExAC	Allele frequency reported in 1000 genome browser	Allele frequency observed in 25 patients in the current study	Allele frequency observed in 30 controls in the current study
Gene	Nucleotide change	AA change	dbSNP ID	ExAC ID	HGMD	Allele frequency reported in ExAC	Allele frequency reported in 1000 genome browser
ABCB11	c.1331 T > C	p.Val444Ala	rs2287622	2:169830328 A/G	CM071525	0.5794	0.5887	0.580 (Homozygous: 9 Heterozygous: 11)	0.667 (Homozygous: 13 Heterozygous 14)
ABCB11	c.1772A > G	p.Asn591Ser	rs11568367	2:169826592 T/C	CM044555	0.0158	0.0310	0.080 (Homozygous: 1 Heterozygous: 2)	0.100 (Homozygous: 0 Heterozygous: 6)
ABCB4	c.1954A > G	p.Arg652Gly	rs2230028	7:87056176 T/C	CM072814	0.1056	0.1703	0.140 (Homozygous: 1 Heterozygous: 5)	0.133 (Homozygous: 1 Heterozygous: 6)

All these variations were predicted to be benign by all the five bioinformatics tools used (Provean, PhD-SNP, SIFT, SNAP, Meta SNP)
^aThis column shows identification details of the particular sequence variant in large-scale human mutation databases, i.e. dbSNP, ExAC, HGMD and ClinVar

ISSN: 1471-230X