rs2834601
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_053277.3(CLIC6):c.*274C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 214,862 control chromosomes in the GnomAD database, including 579 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 0.072 ( 443 hom., cov: 32)
Exomes 𝑓: 0.059 ( 136 hom. )
Consequence
CLIC6
NM_053277.3 3_prime_UTR
NM_053277.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.306
Genes affected
CLIC6 (HGNC:2065): (chloride intracellular channel 6) This gene encodes a member of the chloride intracellular channel family of proteins. The gene is part of a large triplicated region found on chromosomes 1, 6, and 21. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2015]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLIC6 | NM_053277.3 | c.*274C>T | 3_prime_UTR_variant | 6/6 | ENST00000349499.3 | ||
CLIC6 | NM_001317009.2 | c.*274C>T | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLIC6 | ENST00000349499.3 | c.*274C>T | 3_prime_UTR_variant | 6/6 | 1 | NM_053277.3 | P2 | ||
CLIC6 | ENST00000360731.7 | c.*274C>T | 3_prime_UTR_variant | 7/7 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0718 AC: 10893AN: 151632Hom.: 445 Cov.: 32
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GnomAD4 exome AF: 0.0592 AC: 3738AN: 63110Hom.: 136 Cov.: 0 AF XY: 0.0579 AC XY: 1870AN XY: 32288
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GnomAD4 genome ? AF: 0.0718 AC: 10897AN: 151752Hom.: 443 Cov.: 32 AF XY: 0.0710 AC XY: 5261AN XY: 74148
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3478
ClinVar
Not reported inComputational 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