rs7236632
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001374385.1(ATP8B1):c.-25-35138C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,138 control chromosomes in the GnomAD database, including 53,151 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 0.83 ( 53151 hom., cov: 31)
Consequence
ATP8B1
NM_001374385.1 intron
NM_001374385.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.357
Genes affected
ATP8B1 (HGNC:3706): (ATPase phospholipid transporting 8B1) This gene encodes a member of the P-type cation transport ATPase family, which belongs to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Mutations in this gene may result in progressive familial intrahepatic cholestasis type 1 and in benign recurrent intrahepatic cholestasis. [provided by RefSeq, Jul 2008]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8B1 | NM_001374385.1 | c.-25-35138C>T | intron_variant | ENST00000648908.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP8B1 | ENST00000648908.2 | c.-25-35138C>T | intron_variant | NM_001374385.1 | P1 | ||||
ATP8B1 | ENST00000591728.1 | c.-22-35141C>T | intron_variant, NMD_transcript_variant | 3 | |||||
ATP8B1 | ENST00000642462.1 | c.-26+34962C>T | intron_variant, NMD_transcript_variant | ||||||
ATP8B1 | ENST00000648039.1 | c.-25-35138C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.833 AC: 126574AN: 152020Hom.: 53111 Cov.: 31
GnomAD3 genomes
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152020
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.833 AC: 126663AN: 152138Hom.: 53151 Cov.: 31 AF XY: 0.828 AC XY: 61552AN XY: 74372
GnomAD4 genome
?
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126663
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31
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61552
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74372
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2522
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at