rs1541254
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001684.5(ATP2B4):c.-194C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 526,938 control chromosomes in the GnomAD database, including 200,205 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 ( 53348 hom., cov: 31)
Exomes 𝑓: 0.88 ( 146857 hom. )
Consequence
ATP2B4
NM_001684.5 5_prime_UTR
NM_001684.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.477
Genes affected
ATP2B4 (HGNC:817): (ATPase plasma membrane Ca2+ transporting 4) The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 4. Alternatively spliced transcript variants encoding different isoforms have been identified. [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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.-194C>G | 5_prime_UTR_variant | 2/21 | ENST00000357681.10 | ||
ATP2B4 | NM_001001396.3 | c.-194C>G | 5_prime_UTR_variant | 2/22 | |||
ATP2B4 | NM_001365783.2 | c.-194C>G | 5_prime_UTR_variant | 2/21 | |||
ATP2B4 | NM_001365784.2 | c.-194C>G | 5_prime_UTR_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.-194C>G | 5_prime_UTR_variant | 2/21 | 1 | NM_001684.5 | A1 | ||
ATP2B4 | ENST00000341360.7 | c.-194C>G | 5_prime_UTR_variant | 2/22 | 1 | P4 | |||
ATP2B4 | ENST00000705901.1 | c.-194C>G | 5_prime_UTR_variant | 2/21 |
Frequencies
GnomAD3 genomes ? AF: 0.833 AC: 126207AN: 151594Hom.: 53340 Cov.: 31
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GnomAD4 exome AF: 0.883 AC: 331173AN: 375226Hom.: 146857 Cov.: 5 AF XY: 0.883 AC XY: 171907AN XY: 194740
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GnomAD4 genome ? AF: 0.832 AC: 126250AN: 151712Hom.: 53348 Cov.: 31 AF XY: 0.831 AC XY: 61606AN XY: 74134
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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