rs10849577

Positions:

chr12-884848-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_213655.5(WNK1):c.4800C>T(p.Thr1600=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,613,942 control chromosomes in the GnomAD database, including 18,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1468 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16805 hom. )

Consequence

WNK1
NM_213655.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

WNK1 (HGNC:14540): (WNK lysine deficient protein kinase 1) This gene encodes a member of the WNK subfamily of serine/threonine protein kinases. The encoded protein may be a key regulator of blood pressure by controlling the transport of sodium and chloride ions. Mutations in this gene have been associated with pseudohypoaldosteronism type II and hereditary sensory neuropathy type II. Alternatively spliced transcript variants encoding different isoforms have been described but the full-length nature of all of them has yet to be determined.[provided by RefSeq, May 2010]

WNK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 12-884848-C-T is Benign according to our data. Variant chr12-884848-C-T is described in ClinVar as [Benign]. Clinvar id is 137926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-884848-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.049 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WNK1	NM_213655.5 linkuse as main transcript	c.4800C>T	p.Thr1600=	synonymous_variant	19/28	ENST00000340908.9
WNK1	NM_018979.4 linkuse as main transcript	c.4044C>T	p.Thr1348=	synonymous_variant	19/28	ENST00000315939.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WNK1	ENST00000340908.9 linkuse as main transcript	c.4800C>T	p.Thr1600=	synonymous_variant	19/28	5	NM_213655.5	A2	Q9H4A3-5
WNK1	ENST00000315939.11 linkuse as main transcript	c.4044C>T	p.Thr1348=	synonymous_variant	19/28	1	NM_018979.4	P2	Q9H4A3-1

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19293

AN:

151970

Hom.:

1465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0494

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.128

GnomAD3 exomes

AF:

0.156

AC:

39135

AN:

251332

Hom.:

3432

AF XY:

0.159

AC XY:

21633

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.0460

Gnomad AMR exome

AF:

0.122

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.193

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.262

Gnomad NFE exome

AF:

0.153

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.148

AC:

215628

AN:

1461854

Hom.:

16805

Cov.:

AF XY:

0.149

AC XY:

108363

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.0445

Gnomad4 AMR exome

AF:

0.121

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.172

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.144

Gnomad4 OTH exome

AF:

0.151

GnomAD4 genome

AF:

0.127

AC:

19302

AN:

152088

Hom.:

1468

Cov.:

AF XY:

0.132

AC XY:

9803

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0495

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.136

Hom.:

765

Bravo

AF:

0.112

Asia WGS

AF:

0.154

AC:

538

AN:

3478

EpiCase

AF:

0.148

EpiControl

AF:

0.150

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 07, 2014	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Neuropathy, hereditary sensory and autonomic, type 2A

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 12, 2017	- -

Pseudohypoaldosteronism type 2C

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Pseudohypoaldosteronism type 2C;C2752089:Neuropathy, hereditary sensory and autonomic, type 2A

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

not provided

Benign:1

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

-0.85

CADD

Benign

1.9

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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