rs1641511
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001678.5(ATP1B2):c.*464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 171,492 control chromosomes in the GnomAD database, including 44,981 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 0.72 ( 39221 hom., cov: 28)
Exomes 𝑓: 0.75 ( 5760 hom. )
Consequence
ATP1B2
NM_001678.5 3_prime_UTR
NM_001678.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.852
Genes affected
ATP1B2 (HGNC:805): (ATPase Na+/K+ transporting subunit beta 2) The protein encoded by this gene belongs to the family of Na+/K+ and H+/K+ ATPases beta chain proteins, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The beta subunit regulates, through assembly of alpha/beta heterodimers, the number of sodium pumps transported to the plasma membrane. The glycoprotein subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes a beta 2 subunit. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1B2 | NM_001678.5 | c.*464G>A | 3_prime_UTR_variant | 7/7 | ENST00000250111.9 | ||
ATP1B2 | NM_001303263.2 | c.*464G>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1B2 | ENST00000250111.9 | c.*464G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001678.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.716 AC: 108314AN: 151260Hom.: 39190 Cov.: 28
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GnomAD4 exome AF: 0.748 AC: 15039AN: 20114Hom.: 5760 Cov.: 0 AF XY: 0.746 AC XY: 7884AN XY: 10572
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GnomAD4 genome ? AF: 0.716 AC: 108396AN: 151378Hom.: 39221 Cov.: 28 AF XY: 0.717 AC XY: 52975AN XY: 73928
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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