rs7050330
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000369449.7(CLIC2):c.57+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00274 in 1,192,179 control chromosomes in the GnomAD database, including 73 homozygotes. There are 864 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 39 hom., 422 hem., cov: 22)
Exomes 𝑓: 0.0016 ( 34 hom. 442 hem. )
Consequence
CLIC2
ENST00000369449.7 intron
ENST00000369449.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.267
Genes affected
CLIC2 (HGNC:2063): (chloride intracellular channel 2) This gene encodes a chloride intracellular channel protein. Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. This protein plays a role in inhibiting the function of ryanodine receptor 2. A mutation in this gene is the cause of an X-linked form of cognitive disability. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant X-155334361-G-A is Benign according to our data. Variant chrX-155334361-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 446044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLIC2 | NM_001289.6 | c.57+10C>T | intron_variant | ENST00000369449.7 | NP_001280.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLIC2 | ENST00000369449.7 | c.57+10C>T | intron_variant | 1 | NM_001289.6 | ENSP00000358460 | P1 | |||
CLIC2 | ENST00000321926.4 | c.57+10C>T | intron_variant | 3 | ENSP00000318558 | |||||
CLIC2 | ENST00000465553.5 | n.172+10C>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
CLIC2 | ENST00000491205.1 | n.57+10C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0138 AC: 1546AN: 111889Hom.: 39 Cov.: 22 AF XY: 0.0123 AC XY: 422AN XY: 34175
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GnomAD3 exomes AF: 0.00410 AC: 742AN: 181095Hom.: 29 AF XY: 0.00285 AC XY: 191AN XY: 67041
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GnomAD4 exome AF: 0.00159 AC: 1716AN: 1080236Hom.: 34 Cov.: 27 AF XY: 0.00127 AC XY: 442AN XY: 348280
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GnomAD4 genome AF: 0.0138 AC: 1548AN: 111943Hom.: 39 Cov.: 22 AF XY: 0.0123 AC XY: 422AN XY: 34239
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 19, 2017 | - - |
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