Genetic Variant CLCNKB:c.-7-108_-7-107insACACACACACACACACAT (chr1-16044378-C-CACACACACACACACACAT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000085.5(CLCNKB):c.-7-108_-7-107insACACACACACACACACAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0011 ( 18 hom. )

Failed GnomAD Quality Control

Consequence

CLCNKB
NM_000085.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0860

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLCNKB	NM_000085.5 link	c.-7-108_-7-107insACACACACACACACACAT		intron_variant	Intron 1 of 19	ENST00000375679.9	NP_000076.2	P51801-1A8K8H0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLCNKB	ENST00000375679.9 link	c.-7-108_-7-107insACACACACACACACACAT		intron_variant	Intron 1 of 19	1	NM_000085.5	ENSP00000364831.5		P51801-1

Frequencies

GnomAD3 genomes

AF:

0.00147

AC:

222

AN:

151076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000534

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00106

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000631

Gnomad FIN

AF:

0.00326

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00205

Gnomad OTH

AF:

0.00386

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00106

AC:

627

AN:

588808

Hom.:

AF XY:

0.00102

AC XY:

318

AN XY:

312476

show subpopulations

Gnomad4 AFR exome

AF:

0.000225

Gnomad4 AMR exome

AF:

0.00113

Gnomad4 ASJ exome

AF:

0.000802

Gnomad4 EAS exome

AF:

0.0000322

Gnomad4 SAS exome

AF:

0.000811

Gnomad4 FIN exome

AF:

0.00214

Gnomad4 NFE exome

AF:

0.00113

Gnomad4 OTH exome

AF:

0.00116

GnomAD4 genome

AF:

0.00147

AC:

222

AN:

151184

Hom.:

Cov.:

AF XY:

0.00123

AC XY:

AN XY:

73776

show subpopulations

Gnomad4 AFR

AF:

0.000532

Gnomad4 AMR

AF:

0.00106

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000632

Gnomad4 FIN

AF:

0.00326

Gnomad4 NFE

AF:

0.00205

Gnomad4 OTH

AF:

0.00382

Alfa

AF:

0.00172

Hom.:

246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over