rs1200137

Variant names:

• chr1-169111197-T-C
• rs1200137
• NM_001677.4:c.98-173T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-169111197-T-C
• chr1-169111197-T-G

Variant summary

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

The NM_001677.4(ATP1B1):​c.98-173T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,120 control chromosomes in the GnomAD database, including 40,407 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 (40407 hom., cov: 32)
• Consequence: ATP1B1 NM_001677.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001677.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP1B1	NM_001677.4	MANE Select	c.98-173T>C		intron	N/A	NP_001668.1	A3KLL5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP1B1	ENST00000367815.9	TSL:1 MANE Select	c.98-173T>C		intron	N/A	ENSP00000356789.3	P05026-1
	ATP1B1	ENST00000685762.1		c.-244T>C		5_prime_UTR	Exon 1 of 5	ENSP00000508918.1	B7Z9S8
	ATP1B1	ENST00000367816.5	TSL:5	c.98-173T>C		intron	N/A	ENSP00000356790.1	P05026-1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110135 AN: 152002 Hom.: 40388 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.724 AC: 110193 AN: 152120 Hom.: 40407 Cov.: 32 AF XY: 0.729 AC XY: 54219 AN XY: 74350

African (AFR) AF: 0.603 AC: 25027 AN: 41478

American (AMR) AF: 0.759 AC: 11600 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4621 AN: 5184

South Asian (SAS) AF: 0.795 AC: 3833 AN: 4820

European-Finnish (FIN) AF: 0.804 AC: 8496 AN: 10568

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51253 AN: 67994

Other (OTH) AF: 0.755 AC: 1595 AN: 2112

Alfa AF: 0.742 Hom.: 63799

Bravo AF: 0.717

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.88
PromoterAI		-0.022	Neutral
Mutation Taster		=99/1	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: rs1200137; hg19: chr1-169080435;