Variant rs1642763 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001678.5(ATP1B2):c.396A>G(p.Gly132Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,613,966 control chromosomes in the GnomAD database, including 478,665 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 0.80 ( 49011 hom., cov: 31)

Exomes 𝑓: 0.77 ( 429654 hom. )

Consequence

ATP1B2
NM_001678.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.339

Variant links:

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]

ATP1B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP7

Synonymous conserved (PhyloP=-0.339 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP1B2	NM_001678.5 linkuse as main transcript	c.396A>G	p.Gly132Gly	synonymous_variant	4/7	ENST00000250111.9	NP_001669.3	P14415
ATP1B2	NM_001303263.2 linkuse as main transcript	c.150A>G	p.Gly50Gly	synonymous_variant	3/6		NP_001290192.1	P14415

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ATP1B2	ENST00000250111.9 linkuse as main transcript	c.396A>G	p.Gly132Gly	synonymous_variant	4/7	1	NM_001678.5	ENSP00000250111.4	P14415
ATP1B2	ENST00000577026.5 linkuse as main transcript	c.150A>G	p.Gly50Gly	synonymous_variant	3/6	4		ENSP00000459145.1	I3L1V9
ATP1B2	ENST00000577113.1 linkuse as main transcript	c.-10A>G		upstream_gene_variant		3		ENSP00000460499.1	I3L3J8

Frequencies

GnomAD3 genomes

AF:

0.800

AC:

121620

AN:

152002

Hom.:

48964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.884

Gnomad AMI

AF:

0.751

Gnomad AMR

AF:

0.793

Gnomad ASJ

AF:

0.774

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.762

Gnomad MID

AF:

0.924

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.810

GnomAD3 exomes

AF:

0.768

AC:

193043

AN:

251452

Hom.:

74485

AF XY:

0.768

AC XY:

104367

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.887

Gnomad AMR exome

AF:

0.771

Gnomad ASJ exome

AF:

0.775

Gnomad EAS exome

AF:

0.656

Gnomad SAS exome

AF:

0.756

Gnomad FIN exome

AF:

0.750

Gnomad NFE exome

AF:

0.773

Gnomad OTH exome

AF:

0.771

GnomAD4 exome

AF:

0.766

AC:

1119532

AN:

1461846

Hom.:

429654

Cov.:

AF XY:

0.766

AC XY:

557352

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.886

Gnomad4 AMR exome

AF:

0.776

Gnomad4 ASJ exome

AF:

0.776

Gnomad4 EAS exome

AF:

0.632

Gnomad4 SAS exome

AF:

0.760

Gnomad4 FIN exome

AF:

0.749

Gnomad4 NFE exome

AF:

0.766

Gnomad4 OTH exome

AF:

0.778

GnomAD4 genome

AF:

0.800

AC:

121722

AN:

152120

Hom.:

49011

Cov.:

AF XY:

0.798

AC XY:

59369

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.884

Gnomad4 AMR

AF:

0.793

Gnomad4 ASJ

AF:

0.774

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.755

Gnomad4 FIN

AF:

0.762

Gnomad4 NFE

AF:

0.772

Gnomad4 OTH

AF:

0.806

Alfa

AF:

0.778

Hom.:

107833

Bravo

AF:

0.803

Asia WGS

AF:

0.693

AC:

2412

AN:

3478

EpiCase

AF:

0.785

EpiControl

AF:

0.786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

8.0

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over