1-11806284-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000346436.11(CLCN6):c.22C>T(p.Leu8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,502,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L8L) has been classified as Likely benign.
Frequency
Consequence
ENST00000346436.11 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLCN6 | NM_001286.5 | c.22C>T | p.Leu8= | synonymous_variant | 1/23 | ENST00000346436.11 | NP_001277.2 | |
CLCN6 | NM_001256959.2 | c.22C>T | p.Leu8= | synonymous_variant | 1/22 | NP_001243888.2 | ||
CLCN6 | NR_046428.2 | n.94C>T | non_coding_transcript_exon_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLCN6 | ENST00000346436.11 | c.22C>T | p.Leu8= | synonymous_variant | 1/23 | 1 | NM_001286.5 | ENSP00000234488 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000260 AC: 4AN: 153638Hom.: 0 AF XY: 0.0000230 AC XY: 2AN XY: 87126
GnomAD4 exome AF: 0.0000163 AC: 22AN: 1350166Hom.: 0 Cov.: 31 AF XY: 0.0000209 AC XY: 14AN XY: 668316
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74304
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | CLCN6: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at