Variant 19-41966810-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_152296.5(ATP1A3):c.*127A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0035 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ATP1A3
NM_152296.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.112

Variant links:

Genes affected

ATP1A3 (HGNC:801): (ATPase Na+/K+ transporting subunit alpha 3) 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 3 subunit. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ATP1A3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-41966810-T-G is Benign according to our data. Variant chr19-41966810-T-G is described in ClinVar as [Benign]. Clinvar id is 1263673.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
ATP1A3	NM_152296.5 linkuse as main transcript	c.*127A>C	3_prime_UTR_variant	23/23	ENST00000648268.1	NP_689509.1
ATP1A3	NM_001256213.2 linkuse as main transcript	c.*127A>C	3_prime_UTR_variant	23/23		NP_001243142.1
ATP1A3	NM_001256214.2 linkuse as main transcript	c.*127A>C	3_prime_UTR_variant	23/23		NP_001243143.1
ATP1A3	XM_047438862.1 linkuse as main transcript	c.*127A>C	3_prime_UTR_variant	23/23		XP_047294818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP1A3	ENST00000648268.1 linkuse as main transcript	c.*127A>C		3_prime_UTR_variant	23/23		NM_152296.5	ENSP00000498113		P13637-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

2945

AN:

36018

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0836

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0632

Gnomad ASJ

AF:

0.0913

Gnomad EAS

AF:

0.0892

Gnomad SAS

AF:

0.0452

Gnomad FIN

AF:

0.0520

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.0889

Gnomad OTH

AF:

0.101

GnomAD3 exomes

AF:

0.0189

AC:

1924

AN:

101968

Hom.:

AF XY:

0.0170

AC XY:

930

AN XY:

54826

show subpopulations

Gnomad AFR exome

AF:

0.00239

Gnomad AMR exome

AF:

0.000592

Gnomad ASJ exome

AF:

0.00264

Gnomad EAS exome

AF:

0.00350

Gnomad SAS exome

AF:

0.000797

Gnomad FIN exome

AF:

0.162

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00859

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00353

AC:

2591

AN:

733562

Hom.:

Cov.:

AF XY:

0.00345

AC XY:

1246

AN XY:

361216

show subpopulations

Gnomad4 AFR exome

AF:

0.000296

Gnomad4 AMR exome

AF:

0.000325

Gnomad4 ASJ exome

AF:

0.00115

Gnomad4 EAS exome

AF:

0.000336

Gnomad4 SAS exome

AF:

0.00332

Gnomad4 FIN exome

AF:

0.0628

Gnomad4 NFE exome

AF:

0.000841

Gnomad4 OTH exome

AF:

0.00137

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0818

AC:

2951

AN:

36068

Hom.:

Cov.:

AF XY:

0.0791

AC XY:

1364

AN XY:

17244

show subpopulations

Gnomad4 AFR

AF:

0.0838

Gnomad4 AMR

AF:

0.0637

Gnomad4 ASJ

AF:

0.0913

Gnomad4 EAS

AF:

0.0884

Gnomad4 SAS

AF:

0.0462

Gnomad4 FIN

AF:

0.0520

Gnomad4 NFE

AF:

0.0889

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0388

Hom.:

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	clinical testing	GeneDx	Aug 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

8.5

DANN

Benign

0.43

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