rs378538
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000375780.6(CLIC1):c.-412G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 157,080 control chromosomes in the GnomAD database, including 1,203 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 1198 hom., cov: 31)
Exomes 𝑓: 0.051 ( 5 hom. )
Consequence
CLIC1
ENST00000375780.6 5_prime_UTR
ENST00000375780.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.305
Genes affected
CLIC1 (HGNC:2062): (chloride intracellular channel 1) 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. Chloride intracellular channel 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nuclear and plasma membrane chloride ion channel activity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLIC1 | NM_001287593.1 | c.-412G>A | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLIC1 | ENST00000375780.6 | c.-412G>A | 5_prime_UTR_variant | 1/7 | 1 | P1 | |||
CLIC1 | ENST00000395892.5 | c.-50-807G>A | intron_variant | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.107 AC: 16333AN: 151976Hom.: 1199 Cov.: 31
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GnomAD4 exome AF: 0.0509 AC: 254AN: 4986Hom.: 5 Cov.: 3 AF XY: 0.0546 AC XY: 139AN XY: 2544
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GnomAD4 genome ? AF: 0.107 AC: 16334AN: 152094Hom.: 1198 Cov.: 31 AF XY: 0.107 AC XY: 7949AN XY: 74382
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at