chr1-11816605-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001286.5(CLCN6):c.214-10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 1,610,052 control chromosomes in the GnomAD database, including 2,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.044 ( 191 hom., cov: 33)
Exomes 𝑓: 0.050 ( 2069 hom. )
Consequence
CLCN6
NM_001286.5 intron
NM_001286.5 intron
Scores
2
Splicing: ADA: 0.0004344
2
Clinical Significance
Conservation
PhyloP100: -1.69
Genes affected
CLCN6 (HGNC:2024): (chloride voltage-gated channel 6) This gene encodes a member of the voltage-dependent chloride channel protein family. Members of this family can function as either chloride channels or antiporters. This protein is primarily localized to late endosomes and functions as a chloride/proton antiporter. Alternate splicing results in both coding and non-coding variants. Additional alternately spliced variants have been described but their full-length structure is unknown. [provided by RefSeq, Mar 2012]
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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=-0.64).
BP6
Variant 1-11816605-G-A is Benign according to our data. Variant chr1-11816605-G-A is described in ClinVar as [Benign]. Clinvar id is 1601467.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0535 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLCN6 | NM_001286.5 | c.214-10G>A | intron_variant | ENST00000346436.11 | NP_001277.2 | |||
CLCN6 | NM_001256959.2 | c.148-10G>A | intron_variant | NP_001243888.2 | ||||
CLCN6 | NR_046428.2 | n.286-10G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLCN6 | ENST00000346436.11 | c.214-10G>A | intron_variant | 1 | NM_001286.5 | ENSP00000234488.9 |
Frequencies
GnomAD3 genomes AF: 0.0437 AC: 6648AN: 152154Hom.: 191 Cov.: 33
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GnomAD3 exomes AF: 0.0434 AC: 10744AN: 247304Hom.: 328 AF XY: 0.0446 AC XY: 5963AN XY: 133734
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GnomAD4 exome AF: 0.0505 AC: 73614AN: 1457780Hom.: 2069 Cov.: 30 AF XY: 0.0504 AC XY: 36535AN XY: 725064
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GnomAD4 genome AF: 0.0437 AC: 6647AN: 152272Hom.: 191 Cov.: 33 AF XY: 0.0456 AC XY: 3396AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at