chr7-87443361-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000443.4(ABCB4):c.1314G>A(p.Thr438Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00494 in 1,614,046 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000443.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00462 AC: 702AN: 152080Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00463 AC: 1164AN: 251350Hom.: 1 AF XY: 0.00462 AC XY: 627AN XY: 135842
GnomAD4 exome AF: 0.00497 AC: 7268AN: 1461848Hom.: 19 Cov.: 32 AF XY: 0.00481 AC XY: 3499AN XY: 727234
GnomAD4 genome AF: 0.00461 AC: 702AN: 152198Hom.: 6 Cov.: 32 AF XY: 0.00531 AC XY: 395AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:3
ABCB4: BP4, BP7, BS2 -
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not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Cholestasis, intrahepatic, of pregnancy, 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Progressive familial intrahepatic cholestasis type 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at