chrX-50069627-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000307367.2(CLCN5):c.-165C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0118 in 898,734 control chromosomes in the GnomAD database, including 812 homozygotes. There are 2,656 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.057 ( 497 hom., 1665 hem., cov: 23)
Exomes 𝑓: 0.0054 ( 315 hom. 991 hem. )
Consequence
CLCN5
ENST00000307367.2 5_prime_UTR
ENST00000307367.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.306
Genes affected
CLCN5 (HGNC:2023): (chloride voltage-gated channel 5) This gene encodes a member of the ClC family of chloride ion channels and ion transporters. The encoded protein is primarily localized to endosomal membranes and may function to facilitate albumin uptake by the renal proximal tubule. Mutations in this gene have been found in Dent disease and renal tubular disorders complicated by nephrolithiasis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]
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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=-0.85).
BP6
?
Variant X-50069627-C-G is Benign according to our data. Variant chrX-50069627-C-G is described in ClinVar as [Benign]. Clinvar id is 1245383.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN5 | NM_001127898.4 | c.164-252C>G | intron_variant | ENST00000376091.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN5 | ENST00000376091.8 | c.164-252C>G | intron_variant | 2 | NM_001127898.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0572 AC: 6364AN: 111163Hom.: 497 Cov.: 23 AF XY: 0.0499 AC XY: 1667AN XY: 33397
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GnomAD4 exome AF: 0.00537 AC: 4227AN: 787518Hom.: 315 Cov.: 23 AF XY: 0.00444 AC XY: 991AN XY: 223054
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GnomAD4 genome ? AF: 0.0572 AC: 6361AN: 111216Hom.: 497 Cov.: 23 AF XY: 0.0498 AC XY: 1665AN XY: 33460
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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 | Sep 18, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at