rs515726132
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_004366.6(CLCN2):c.221-14_221-4del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
CLCN2
NM_004366.6 splice_region, splice_polypyrimidine_tract, intron
NM_004366.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.47
Genes affected
CLCN2 (HGNC:2020): (chloride voltage-gated channel 2) This gene encodes a voltage-gated chloride channel. The encoded protein is a transmembrane protein that maintains chloride ion homeostasis in various cells. Defects in this gene may be a cause of certain epilepsies. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 3-184358816-GGGTGCAGGGAA-G is Benign according to our data. Variant chr3-184358816-GGGTGCAGGGAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 9036.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN2 | NM_004366.6 | c.221-14_221-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000265593.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN2 | ENST00000265593.9 | c.221-14_221-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004366.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Leukoencephalopathy with mild cerebellar ataxia and white matter edema Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | GeneReviews | Sep 09, 2015 | - - |
Epilepsy, idiopathic generalized, susceptibility to, 11 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Sep 01, 2009 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 19, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at