rs12591825
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024837.4(ATP8B4):c.363-8021G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,230,510 control chromosomes in the GnomAD database, including 158,779 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.58 ( 27071 hom., cov: 33)
Exomes 𝑓: 0.47 ( 131708 hom. )
Consequence
ATP8B4
NM_024837.4 intron
NM_024837.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.266
Genes affected
ATP8B4 (HGNC:13536): (ATPase phospholipid transporting 8B4 (putative)) This gene encodes a member of the cation transport ATPase (P-type) family and type IV subfamily. The encoded protein is involved in phospholipid transport in the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8B4 | NM_024837.4 | c.363-8021G>T | intron_variant | ENST00000284509.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP8B4 | ENST00000284509.11 | c.363-8021G>T | intron_variant | 5 | NM_024837.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.578 AC: 87879AN: 151948Hom.: 27022 Cov.: 33
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GnomAD3 exomes AF: 0.608 AC: 77813AN: 127984Hom.: 25891 AF XY: 0.605 AC XY: 42374AN XY: 70088
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GnomAD4 exome AF: 0.475 AC: 511781AN: 1078444Hom.: 131708 Cov.: 28 AF XY: 0.483 AC XY: 256781AN XY: 531492
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GnomAD4 genome ? AF: 0.579 AC: 87992AN: 152066Hom.: 27071 Cov.: 33 AF XY: 0.586 AC XY: 43584AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at