rs2297727
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000085.5(CLCNKB):c.1845+68C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,570,726 control chromosomes in the GnomAD database, including 173,331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.43 ( 14487 hom., cov: 31)
Exomes 𝑓: 0.47 ( 158844 hom. )
Consequence
CLCNKB
NM_000085.5 intron
NM_000085.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.21
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 1-16055591-C-T is Benign according to our data. Variant chr1-16055591-C-T is described in ClinVar as [Benign]. Clinvar id is 1229089.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCNKB | NM_000085.5 | c.1845+68C>T | intron_variant | ENST00000375679.9 | |||
CLCNKB | NM_001165945.2 | c.1338+68C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCNKB | ENST00000375679.9 | c.1845+68C>T | intron_variant | 1 | NM_000085.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.426 AC: 64478AN: 151508Hom.: 14479 Cov.: 31
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GnomAD4 exome AF: 0.468 AC: 664408AN: 1419100Hom.: 158844 Cov.: 25 AF XY: 0.468 AC XY: 331124AN XY: 707604
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GnomAD4 genome ? AF: 0.425 AC: 64505AN: 151626Hom.: 14487 Cov.: 31 AF XY: 0.428 AC XY: 31740AN XY: 74088
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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
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at