rs1200131

Variant names:

• chr1-169109621-G-A
• rs1200131
• NM_001677.4:c.98-1749G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001677.4(ATP1B1):​c.98-1749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,014 control chromosomes in the GnomAD database, including 8,702 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 0.33 (8702 hom., cov: 32)
• Consequence: ATP1B1 NM_001677.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 6 publications found

Genes affected

ATP1B1 (HGNC:804): (ATPase Na+/K+ transporting subunit beta 1) 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 1 subunit. Alternatively spliced transcript variants encoding different isoforms have been described, but their biological validity is not known. [provided by RefSeq, Mar 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP1B1	NM_001677.4	c.98-1749G>A		intron_variant	Intron 1 of 5	ENST00000367815.9	NP_001668.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP1B1	ENST00000367815.9	c.98-1749G>A		intron_variant	Intron 1 of 5	1	NM_001677.4	ENSP00000356789.3

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49615 AN: 151896 Hom.: 8681 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.278

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.327 AC: 49684 AN: 152014 Hom.: 8702 Cov.: 32 AF XY: 0.324 AC XY: 24061 AN XY: 74286

African (AFR) AF: 0.426 AC: 17637 AN: 41428

American (AMR) AF: 0.230 AC: 3512 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3466

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4826

European-Finnish (FIN) AF: 0.375 AC: 3955 AN: 10550

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21219 AN: 67970

Other (OTH) AF: 0.280 AC: 591 AN: 2110

Alfa AF: 0.311 Hom.: 9450

Bravo AF: 0.318

Asia WGS AF: 0.170 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.051
DANN	Benign	0.85
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1200131; hg19: chr1-169078859;