NM_000053.4:c.1544-53A>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000053.4(ATP7B):c.1544-53A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 1,598,864 control chromosomes in the GnomAD database, including 387,838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000053.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP7B | NM_000053.4 | c.1544-53A>C | intron_variant | Intron 3 of 20 | ENST00000242839.10 | NP_000044.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.689 AC: 104539AN: 151754Hom.: 36289 Cov.: 30
GnomAD4 exome AF: 0.694 AC: 1003998AN: 1446992Hom.: 351512 AF XY: 0.689 AC XY: 496490AN XY: 720834
GnomAD4 genome AF: 0.689 AC: 104630AN: 151872Hom.: 36326 Cov.: 30 AF XY: 0.685 AC XY: 50798AN XY: 74188
ClinVar
Submissions by phenotype
Wilson disease Benign:2
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not provided 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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at