rs114702742
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004366.6(CLCN2):c.2173C>T(p.Arg725Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000795 in 1,613,196 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004366.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00394 AC: 600AN: 152238Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00100 AC: 250AN: 249636Hom.: 1 AF XY: 0.000738 AC XY: 100AN XY: 135450
GnomAD4 exome AF: 0.000467 AC: 682AN: 1460840Hom.: 4 Cov.: 32 AF XY: 0.000407 AC XY: 296AN XY: 726728
GnomAD4 genome AF: 0.00394 AC: 600AN: 152356Hom.: 4 Cov.: 32 AF XY: 0.00365 AC XY: 272AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:4
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CLCN2: BS1, BS2 -
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Leukoencephalopathy with mild cerebellar ataxia and white matter edema Benign:1Other:1
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CLCN2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at