rs748214
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000704.3(ATP4A):c.1501-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,060,460 control chromosomes in the GnomAD database, including 57,848 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 0.28 ( 6608 hom., cov: 23)
Exomes 𝑓: 0.28 ( 51240 hom. )
Consequence
ATP4A
NM_000704.3 intron
NM_000704.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.363
Genes affected
ATP4A (HGNC:819): (ATPase H+/K+ transporting subunit alpha) The protein encoded by this gene belongs to a family of P-type cation-transporting ATPases. The gastric H+, K+-ATPase is a heterodimer consisting of a high molecular weight catalytic alpha subunit and a smaller but heavily glycosylated beta subunit. This enzyme is a proton pump that catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. It is also responsible for gastric acid secretion. This gene encodes a catalytic alpha subunit of the gastric H+, K+-ATPase. [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=-0.75).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP4A | NM_000704.3 | c.1501-42C>T | intron_variant | ENST00000262623.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP4A | ENST00000262623.4 | c.1501-42C>T | intron_variant | 1 | NM_000704.3 | P1 | |||
ENST00000702449.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 41499AN: 146524Hom.: 6610 Cov.: 23
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GnomAD3 exomes AF: 0.233 AC: 8600AN: 36950Hom.: 1663 AF XY: 0.247 AC XY: 4784AN XY: 19386
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GnomAD4 exome AF: 0.278 AC: 254266AN: 913830Hom.: 51240 Cov.: 13 AF XY: 0.284 AC XY: 127610AN XY: 449648
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GnomAD4 genome ? AF: 0.283 AC: 41498AN: 146630Hom.: 6608 Cov.: 23 AF XY: 0.281 AC XY: 20042AN XY: 71346
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ClinVar
Not reported inComputational scores
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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