NM_213655.5:c.1479T>C

Variant names:

Variant summary

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

The NM_213655.5(WNK1):c.1479T>C(p.Asp493Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,612,990 control chromosomes in the GnomAD database, including 19,482 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1489 hom., cov: 31)

Exomes 𝑓: 0.15 ( 17993 hom. )

Consequence

WNK1
NM_213655.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.615

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=-0.55).

BP6

Variant 12-859323-T-C is Benign according to our data. Variant chr12-859323-T-C is described in ClinVar as [Benign]. Clinvar id is 137923.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-859323-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.615 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WNK1	NM_213655.5 link	c.1479T>C	p.Asp493Asp	synonymous_variant	Exon 6 of 28	ENST00000340908.9	NP_998820.3	Q9H4A3-5
WNK1	NM_018979.4 link	c.1479T>C	p.Asp493Asp	synonymous_variant	Exon 6 of 28	ENST00000315939.11	NP_061852.3	Q9H4A3-1A5D8Z4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WNK1	ENST00000340908.9 link	c.1479T>C	p.Asp493Asp	synonymous_variant	Exon 6 of 28	5	NM_213655.5	ENSP00000341292.5		Q9H4A3-5
WNK1	ENST00000315939.11 link	c.1479T>C	p.Asp493Asp	synonymous_variant	Exon 6 of 28	1	NM_018979.4	ENSP00000313059.6		Q9H4A3-1

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19086

AN:

151916

Hom.:

1488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0504

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.0900

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0614

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.122

GnomAD3 exomes

AF:

0.146

AC:

36681

AN:

250580

Hom.:

3333

AF XY:

0.154

AC XY:

20849

AN XY:

135508

show subpopulations

Gnomad AFR exome

AF:

0.0473

Gnomad AMR exome

AF:

0.0692

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.0672

Gnomad SAS exome

AF:

0.182

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.162

Gnomad OTH exome

AF:

0.160

GnomAD4 exome

AF:

0.151

AC:

220517

AN:

1460956

Hom.:

17993

Cov.:

AF XY:

0.153

AC XY:

111195

AN XY:

726800

show subpopulations

Gnomad4 AFR exome

AF:

0.0455

Gnomad4 AMR exome

AF:

0.0713

Gnomad4 ASJ exome

AF:

0.153

Gnomad4 EAS exome

AF:

0.0488

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.126

AC:

19098

AN:

152034

Hom.:

1489

Cov.:

AF XY:

0.130

AC XY:

9659

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.0506

Gnomad4 AMR

AF:

0.0899

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0615

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.148

Hom.:

4151

Bravo

AF:

0.107

Asia WGS

AF:

0.107

AC:

371

AN:

3476

EpiCase

AF:

0.154

EpiControl

AF:

0.159

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 07, 2014

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Neuropathy, hereditary sensory and autonomic, type 2A

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 12, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Pseudohypoaldosteronism type 2C

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

6.6

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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