rs747118105
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PP2PP3_ModerateBP6BS2
The NM_001830.4(CLCN4):āc.1937T>Cā(p.Ile646Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000176 in 1,079,046 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001830.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCN4 | NM_001830.4 | c.1937T>C | p.Ile646Thr | missense_variant | 11/13 | ENST00000380833.9 | |
CLCN4 | NM_001256944.2 | c.1655T>C | p.Ile552Thr | missense_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN4 | ENST00000380833.9 | c.1937T>C | p.Ile646Thr | missense_variant | 11/13 | 1 | NM_001830.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD3 exomes AF: 0.0000949 AC: 15AN: 158041Hom.: 0 AF XY: 0.0000822 AC XY: 4AN XY: 48647
GnomAD4 exome AF: 0.0000176 AC: 19AN: 1079046Hom.: 0 Cov.: 31 AF XY: 0.0000172 AC XY: 6AN XY: 348848
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at