rs3831297
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_016929.5(CLIC5):c.589-9_589-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,573,906 control chromosomes in the GnomAD database, including 111,011 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.34 ( 8909 hom., cov: 0)
Exomes 𝑓: 0.38 ( 102102 hom. )
Consequence
CLIC5
NM_016929.5 splice_region, splice_polypyrimidine_tract, intron
NM_016929.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.51
Genes affected
CLIC5 (HGNC:13517): (chloride intracellular channel 5) This gene encodes a member of the chloride intracellular channel (CLIC) family of chloride ion channels. The encoded protein associates with actin-based cytoskeletal structures and may play a role in multiple processes including hair cell stereocilia formation, myoblast proliferation and glomerular podocyte and endothelial cell maintenance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 6-45903262-CAG-C is Benign according to our data. Variant chr6-45903262-CAG-C is described in ClinVar as [Benign]. Clinvar id is 506168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLIC5 | NM_016929.5 | c.589-9_589-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000339561.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLIC5 | ENST00000339561.12 | c.589-9_589-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016929.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.338 AC: 51253AN: 151752Hom.: 8905 Cov.: 0
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GnomAD3 exomes AF: 0.354 AC: 75576AN: 213610Hom.: 13882 AF XY: 0.363 AC XY: 41223AN XY: 113578
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GnomAD4 exome AF: 0.376 AC: 534338AN: 1422036Hom.: 102102 AF XY: 0.377 AC XY: 264972AN XY: 702708
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GnomAD4 genome ? AF: 0.338 AC: 51274AN: 151870Hom.: 8909 Cov.: 0 AF XY: 0.338 AC XY: 25083AN XY: 74188
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Sep 25, 2017 | c.1066-9_1066-8delCT in intron 5 of CLIC5: This variant is not expected to have clinical significance because it has been identified in 44.4% (8056/18162) of Ea st Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.b roadinstitute.org/; dbSNP rs35735653). - |
Computational scores
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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