20-45095047-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001322799.2(KCNS1):c.1404G>T(p.Lys468Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001322799.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNS1 | ENST00000537075.3 | c.1404G>T | p.Lys468Asn | missense_variant | Exon 4 of 4 | 1 | NM_001322799.2 | ENSP00000445595.1 | ||
KCNS1 | ENST00000306117.5 | c.1404G>T | p.Lys468Asn | missense_variant | Exon 5 of 5 | 1 | ENSP00000307694.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251354Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135834
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461754Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 76AN XY: 727170
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1404G>T (p.K468N) alteration is located in exon 5 (coding exon 3) of the KCNS1 gene. This alteration results from a G to T substitution at nucleotide position 1404, causing the lysine (K) at amino acid position 468 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at