chrX-10185083-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001830.4(CLCN4):c.51C>T(p.Leu17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,207,309 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L17L) has been classified as Likely benign.
Frequency
Consequence
NM_001830.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN4 | NM_001830.4 | c.51C>T | p.Leu17= | synonymous_variant | 3/13 | ENST00000380833.9 | |
CLCN4 | NM_001256944.2 | c.-38-9828C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN4 | ENST00000380833.9 | c.51C>T | p.Leu17= | synonymous_variant | 3/13 | 1 | NM_001830.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000449 AC: 5AN: 111326Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33554
GnomAD3 exomes AF: 0.0000438 AC: 8AN: 182576Hom.: 0 AF XY: 0.0000448 AC XY: 3AN XY: 67034
GnomAD4 exome AF: 0.0000283 AC: 31AN: 1095930Hom.: 0 Cov.: 29 AF XY: 0.0000332 AC XY: 12AN XY: 361366
GnomAD4 genome ? AF: 0.0000449 AC: 5AN: 111379Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33617
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at