rs10797059

chr1-160132466-A-Gchr1-160132466-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000702.4(ATP1A2):c.1827+1869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,074 control chromosomes in the GnomAD database, including 50,115 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 0.81 (50115 hom., cov: 30)
• Consequence: ATP1A2 NM_000702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

ATP1A2 (HGNC:800): (ATPase Na+/K+ transporting subunit alpha 2) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, 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 catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 2 subunit. Mutations in this gene result in familial basilar or hemiplegic migraines, and in a rare syndrome known as alternating hemiplegia of childhood. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP1A2	NM_000702.4	c.1827+1869A>G		intron_variant		ENST00000361216.8
ATP1A2	XM_047421286.1	c.936+1869A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP1A2	ENST00000361216.8	c.1827+1869A>G		intron_variant		1	NM_000702.4	P1
ATP1A2	ENST00000392233.7	c.1827+1869A>G		intron_variant		5
ATP1A2	ENST00000447527.1	c.959+1869A>G		intron_variant		2
ATP1A2	ENST00000472488.5	n.1930+1869A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122966 AN: 151956 Hom.: 50104 Cov.: 30

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.809 AC: 123022 AN: 152074 Hom.: 50115 Cov.: 30 AF XY: 0.807 AC XY: 59985 AN XY: 74338

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.795

Alfa AF: 0.847 Hom.: 72670

Bravo AF: 0.790

Asia WGS AF: 0.755 AC: 2628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.82

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

Other links and lift over

dbSNP: rs10797059; hg19: chr1-160102256;