rs12912519
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000558829.1(ATP8B4):c.-42-34315A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,476 control chromosomes in the GnomAD database, including 5,662 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 0.25 ( 5662 hom., cov: 30)
Consequence
ATP8B4
ENST00000558829.1 intron
ENST00000558829.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.42
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=-0.98).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP8B4 | XM_011522056.4 | c.-42-34315A>C | intron_variant | ||||
ATP8B4 | XM_017022587.3 | c.-42-34315A>C | intron_variant | ||||
ATP8B4 | XM_047433096.1 | c.-42-34315A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP8B4 | ENST00000558829.1 | c.-42-34315A>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.254 AC: 38479AN: 151358Hom.: 5661 Cov.: 30
GnomAD3 genomes
?
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.254 AC: 38498AN: 151476Hom.: 5662 Cov.: 30 AF XY: 0.256 AC XY: 18925AN XY: 73956
GnomAD4 genome
?
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38498
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30
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18925
AN XY:
73956
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401
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at