NM_000085.5:c.-7-108_-7-107insACAT

Variant names:

• chr1-16044378-C-CACAT
• rs146972886
• NM_000085.5:c.-7-108_-7-107insACAT

Variant summary

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

The NM_000085.5(CLCNKB):​c.-7-108_-7-107insACAT 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 0.00018 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0018 (37 hom.)
  • Failed GnomAD Quality Control
• Consequence: CLCNKB NM_000085.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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]

ACMG classification

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	c.-7-108_-7-107insACAT		intron_variant	Intron 1 of 19	ENST00000375679.9	NP_000076.2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000179 AC: 27 AN: 151074 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00106

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000192

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.000482

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00183 AC: 1076 AN: 588508 Hom.: 37 AF XY: 0.00185 AC XY: 579 AN XY: 312296

Gnomad4 AFR exome AF: 0.000281

Gnomad4 AMR exome AF: 0.00438

Gnomad4 ASJ exome AF: 0.00488

Gnomad4 EAS exome AF: 0.000323

Gnomad4 SAS exome AF: 0.00167

Gnomad4 FIN exome AF: 0.00216

Gnomad4 NFE exome AF: 0.00161

Gnomad4 OTH exome AF: 0.00197

GnomAD4 genome AF: 0.000179 AC: 27 AN: 151074 Hom.: 0 Cov.: 0 AF XY: 0.000176 AC XY: 13 AN XY: 73656

Gnomad4 AFR AF: 0.0000243

Gnomad4 AMR AF: 0.00106

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000192

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.000482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs146972886; hg19: chr1-16370873;