2-168923626-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM1BP4_ModerateBP6BS2
The NM_003742.4(ABCB11):c.3962G>A(p.Ser1321Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000713 in 1,613,782 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003742.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 151966Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000144 AC: 36AN: 249214Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135206
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461698Hom.: 3 Cov.: 31 AF XY: 0.000110 AC XY: 80AN XY: 727134
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152084Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 28733223) -
ABCB11-related disorder Uncertain:1
The ABCB11 c.3962G>A variant is predicted to result in the amino acid substitution p.Ser1321Asn. This variant was reported in the heterozygous state in an individual with progressive familial intrahepatic cholestasis (Table S2, Dröge et al. 2017. PubMed ID: 28733223). This variant is reported in 0.12% of alleles in individuals of South Asian descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Progressive familial intrahepatic cholestasis type 2 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at