Variant chr1-16044238-CAG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLCNKB	NM_000085.5 link	c.-7-247_-7-246delAG		intron_variant		ENST00000375679.9	NP_000076.2	P51801-1A8K8H0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLCNKB	ENST00000375679.9 link	c.-7-247_-7-246delAG		intron_variant		1	NM_000085.5	ENSP00000364831.5		P51801-1

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

Gnomad4 AFR

AF:

0.280

Gnomad4 AMR

AF:

0.662

Gnomad4 ASJ

AF:

0.673

Gnomad4 EAS

AF:

0.702

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.566

Gnomad4 NFE

AF:

0.642

Gnomad4 OTH

AF:

0.594

Alfa

AF:

0.587

Hom.:

3361

Bravo

AF:

0.540

Asia WGS

AF:

0.633

AC:

2196

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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