dbSNP rs1641511: ATP1B2:c.*464G>A (chr17-7656359-G-A) – ACMG Classification: Benign (-12 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.852

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:

Genome browser will be placed here

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 rank	MANE	Protein	UniProt
ATP1B2	NM_001678.5 link	c.*464G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000250111.9	NP_001669.3	P14415
ATP1B2	NM_001303263.2 link	c.*464G>A		3_prime_UTR_variant	Exon 6 of 6		NP_001290192.1	P14415

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP1B2	ENST00000250111.9 link	c.*464G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_001678.5	ENSP00000250111.4		P14415

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108314

AN:

151260

Hom.:

39190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.606

Gnomad AMI

AF:

0.749

Gnomad AMR

AF:

0.756

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.646

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.741

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.744

GnomAD4 exome

AF:

0.748

AC:

15039

AN:

20114

Hom.:

5760

Cov.:

AF XY:

0.746

AC XY:

7884

AN XY:

10572

show subpopulations

Gnomad4 AFR exome

AF:

0.578

Gnomad4 AMR exome

AF:

0.772

Gnomad4 ASJ exome

AF:

0.787

Gnomad4 EAS exome

AF:

0.634

Gnomad4 SAS exome

AF:

0.715

Gnomad4 FIN exome

AF:

0.748

Gnomad4 NFE exome

AF:

0.768

Gnomad4 OTH exome

AF:

0.755

GnomAD4 genome

AF:

0.716

AC:

108396

AN:

151378

Hom.:

39221

Cov.:

AF XY:

0.717

AC XY:

52975

AN XY:

73928

show subpopulations

Gnomad4 AFR

AF:

0.607

Gnomad4 AMR

AF:

0.756

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.645

Gnomad4 SAS

AF:

0.726

Gnomad4 FIN

AF:

0.741

Gnomad4 NFE

AF:

0.769

Gnomad4 OTH

AF:

0.740

Alfa

AF:

0.763

Hom.:

74746

Bravo

AF:

0.708

Asia WGS

AF:

0.656

AC:

2282

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.56

DANN

Benign

0.71

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