rs16963067
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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.2036-22A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,606,320 control chromosomes in the GnomAD database, including 26,435 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 0.23 ( 5881 hom., cov: 32)
Exomes 𝑓: 0.16 ( 20554 hom. )
Consequence
ATP8B4
NM_024837.4 intron
NM_024837.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.869
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8B4 | NM_024837.4 | c.2036-22A>G | intron_variant | ENST00000284509.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP8B4 | ENST00000284509.11 | c.2036-22A>G | intron_variant | 5 | NM_024837.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.232 AC: 35219AN: 152024Hom.: 5875 Cov.: 32
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GnomAD3 exomes AF: 0.149 AC: 37306AN: 250682Hom.: 4072 AF XY: 0.146 AC XY: 19833AN XY: 135476
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GnomAD4 exome AF: 0.156 AC: 227573AN: 1454178Hom.: 20554 Cov.: 29 AF XY: 0.157 AC XY: 113410AN XY: 723984
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GnomAD4 genome ? AF: 0.232 AC: 35264AN: 152142Hom.: 5881 Cov.: 32 AF XY: 0.224 AC XY: 16631AN XY: 74386
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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