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

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

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