rs202146217
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_000443.4(ABCB4):c.833+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000394 in 1,614,128 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000443.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCB4 | NM_000443.4 | c.833+6G>A | splice_region_variant, intron_variant | ENST00000649586.2 | NP_000434.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCB4 | ENST00000649586.2 | c.833+6G>A | splice_region_variant, intron_variant | NM_000443.4 | ENSP00000496956.2 |
Frequencies
GnomAD3 genomes AF: 0.000611 AC: 93AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00168 AC: 423AN: 251288Hom.: 4 AF XY: 0.00124 AC XY: 168AN XY: 135808
GnomAD4 exome AF: 0.000372 AC: 544AN: 1461818Hom.: 3 Cov.: 31 AF XY: 0.000300 AC XY: 218AN XY: 727218
GnomAD4 genome AF: 0.000604 AC: 92AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 02, 2018 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 21, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at