dbSNP rs138811867: CLCNKB:c.-7-247_-7-246delAG (chr1-16044238-CAG-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000085.5(CLCNKB):c.-7-247_-7-246delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 24591 hom., cov: 0)

Consequence

CLCNKB
NM_000085.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0240

Publications

0 publications found

Variant links:

Genes affected

CLCNKB (HGNC:2027): (chloride voltage-gated channel Kb) The protein encoded by this gene is a member of the family of voltage-gated chloride channels. Chloride channels have several functions, including the regulation of cell volume, membrane potential stabilization, signal transduction and transepithelial transport. This gene is expressed predominantly in the kidney and may be important for renal salt reabsorption. Mutations in this gene are associated with autosomal recessive Bartter syndrome type 3 (BS3). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

CLCNKB Gene-Disease associations (from GenCC):

Bartter disease type 3
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
Bartter disease type 4B
Inheritance: AR Classification: STRONG Submitted by: G2P
Bartter syndrome type 4
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Gitelman syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CLCNKB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 1-16044238-CAG-C is Benign according to our data. Variant chr1-16044238-CAG-C is described in ClinVar as Benign. ClinVar VariationId is 1228357.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000085.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLCNKB	NM_000085.5	MANE Select	c.-7-247_-7-246delAG		intron	N/A	NP_000076.2	P51801-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CLCNKB	ENST00000375679.9	TSL:1 MANE Select	c.-7-247_-7-246delAG	intron	N/A	ENSP00000364831.5	P51801-1
CLCNKB	ENST00000906263.1		c.-7-247_-7-246delAG	intron	N/A	ENSP00000576322.1
CLCNKB	ENST00000906270.1		c.-7-247_-7-246delAG	intron	N/A	ENSP00000576329.1

Frequencies

GnomAD3 genomes

AF:

0.545

AC:

82564

AN:

151610

Hom.:

24575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.662

Gnomad ASJ

AF:

0.673

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.681

Gnomad FIN

AF:

0.566

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.642

Gnomad OTH

AF:

0.590

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

GnomAD4 genome

AF:

0.544

AC:

82602

AN:

151728

Hom.:

24591

Cov.:

AF XY:

0.547

AC XY:

40551

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.280

AC:

11572

AN:

41328

American (AMR)

AF:

0.662

AC:

10112

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.673

AC:

2332

AN:

3466

East Asian (EAS)

AF:

0.702

AC:

3610

AN:

5144

South Asian (SAS)

AF:

0.682

AC:

3276

AN:

4804

European-Finnish (FIN)

AF:

0.566

AC:

5972

AN:

10542

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.642

AC:

43585

AN:

67862

Other (OTH)

AF:

0.594

AC:

1250

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1618

3236

4855

6473

8091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

706

1412

2118

2824

3530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.587

Hom.:

3361

Bravo

AF:

0.540

Asia WGS

AF:

0.633

AC:

2196

AN:

3474

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.024

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over