rs5255
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000085.5(CLCNKB):c.1979C>T(p.Ser660Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,597,122 control chromosomes in the GnomAD database, including 129 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000085.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCNKB | NM_000085.5 | c.1979C>T | p.Ser660Leu | missense_variant | 19/20 | ENST00000375679.9 | |
CLCNKB | NM_001165945.2 | c.1469C>T | p.Ser490Leu | missense_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCNKB | ENST00000375679.9 | c.1979C>T | p.Ser660Leu | missense_variant | 19/20 | 1 | NM_000085.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0150 AC: 2254AN: 150690Hom.: 56 Cov.: 29
GnomAD3 exomes AF: 0.00397 AC: 997AN: 251220Hom.: 21 AF XY: 0.00282 AC XY: 383AN XY: 135788
GnomAD4 exome AF: 0.00159 AC: 2306AN: 1446308Hom.: 72 Cov.: 35 AF XY: 0.00136 AC XY: 977AN XY: 719176
GnomAD4 genome ? AF: 0.0150 AC: 2269AN: 150814Hom.: 57 Cov.: 29 AF XY: 0.0145 AC XY: 1067AN XY: 73650
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at