rs762119830
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004070.4(CLCNKA):c.1613G>A(p.Arg538His) variant causes a missense change. The variant allele was found at a frequency of 0.0000123 in 1,460,906 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R538C) has been classified as Likely benign.
Frequency
Consequence
NM_004070.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCNKA | NM_004070.4 | c.1613G>A | p.Arg538His | missense_variant | 15/20 | ENST00000331433.5 | |
CLCNKA | NM_001042704.2 | c.1613G>A | p.Arg538His | missense_variant | 15/20 | ||
CLCNKA | NM_001257139.2 | c.1484G>A | p.Arg495His | missense_variant | 14/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCNKA | ENST00000331433.5 | c.1613G>A | p.Arg538His | missense_variant | 15/20 | 1 | NM_004070.4 | P4 | |
CLCNKA | ENST00000375692.5 | c.1613G>A | p.Arg538His | missense_variant | 16/21 | 1 | A1 | ||
CLCNKA | ENST00000439316.6 | c.1484G>A | p.Arg495His | missense_variant | 14/19 | 2 | |||
CLCNKA | ENST00000464764.5 | n.2217G>A | non_coding_transcript_exon_variant | 19/24 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249834Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135382
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460906Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726762
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at