Variant 1-116373434-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBA1

The NM_000701.8(ATP1A1):c.-78C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 1,464,764 control chromosomes in the GnomAD database, including 12,073 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 5622 hom., cov: 31)

Exomes 𝑓: 0.072 ( 6451 hom. )

Consequence

ATP1A1
NM_000701.8 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

ATP1A1 (HGNC:799): (ATPase Na+/K+ transporting subunit alpha 1) 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 1 subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

ATP1A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.11).

BP6

Variant 1-116373434-C-T is Benign according to our data. Variant chr1-116373434-C-T is described in ClinVar as [Benign]. Clinvar id is 1177949.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP1A1	NM_000701.8 linkuse as main transcript	c.-78C>T		5_prime_UTR_variant	1/23	ENST00000295598.10	NP_000692.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP1A1	ENST00000295598.10 linkuse as main transcript	c.-78C>T	5_prime_UTR_variant	1/23	1	NM_000701.8	ENSP00000295598	P4	P05023-1
ATP1A1	ENST00000418797.5 linkuse as main transcript	c.-82+513C>T	intron_variant		3		ENSP00000400124
ATP1A1	ENST00000488733.1 linkuse as main transcript	n.166C>T	non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28731

AN:

151628

Hom.:

5599

Cov.:

show subpopulations

Gnomad AFR

AF:

0.496

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0845

Gnomad EAS

AF:

0.0990

Gnomad SAS

AF:

0.0883

Gnomad FIN

AF:

0.0250

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.0593

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.0849

AC:

7950

AN:

93608

Hom.:

630

AF XY:

0.0823

AC XY:

4325

AN XY:

52582

show subpopulations

Gnomad AFR exome

AF:

0.529

Gnomad AMR exome

AF:

0.147

Gnomad ASJ exome

AF:

0.0819

Gnomad EAS exome

AF:

0.0876

Gnomad SAS exome

AF:

0.0885

Gnomad FIN exome

AF:

0.0261

Gnomad NFE exome

AF:

0.0558

Gnomad OTH exome

AF:

0.0933

GnomAD4 exome

AF:

0.0716

AC:

94078

AN:

1313024

Hom.:

6451

Cov.:

AF XY:

0.0710

AC XY:

46055

AN XY:

648294

show subpopulations

Gnomad4 AFR exome

AF:

0.509

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.0824

Gnomad4 EAS exome

AF:

0.0857

Gnomad4 SAS exome

AF:

0.0925

Gnomad4 FIN exome

AF:

0.0292

Gnomad4 NFE exome

AF:

0.0572

Gnomad4 OTH exome

AF:

0.0956

GnomAD4 genome

AF:

0.190

AC:

28798

AN:

151740

Hom.:

5622

Cov.:

AF XY:

0.185

AC XY:

13749

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.145

Gnomad4 ASJ

AF:

0.0845

Gnomad4 EAS

AF:

0.0993

Gnomad4 SAS

AF:

0.0869

Gnomad4 FIN

AF:

0.0250

Gnomad4 NFE

AF:

0.0593

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.115

Hom.:

444

Bravo

AF:

0.213

Asia WGS

AF:

0.114

AC:

397

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.11

CADD

Benign

DANN

Benign

0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over