8-98428037-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020697.4(KCNS2):c.58C>T(p.Arg20Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,608,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020697.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCNS2 | NM_020697.4 | c.58C>T | p.Arg20Cys | missense_variant | Exon 2 of 2 | ENST00000287042.5 | NP_065748.1 | |
STK3 | XM_047422133.1 | c.1423+9066G>A | intron_variant | Intron 11 of 11 | XP_047278089.1 | |||
STK3 | XR_007060752.1 | n.1571+9066G>A | intron_variant | Intron 11 of 14 | ||||
STK3 | XR_007060753.1 | n.1571+9066G>A | intron_variant | Intron 11 of 12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNS2 | ENST00000287042.5 | c.58C>T | p.Arg20Cys | missense_variant | Exon 2 of 2 | 1 | NM_020697.4 | ENSP00000287042.4 | ||
KCNS2 | ENST00000521839.1 | c.58C>T | p.Arg20Cys | missense_variant | Exon 2 of 2 | 5 | ENSP00000430712.1 | |||
STK3 | ENST00000517832.1 | n.483+6090G>A | intron_variant | Intron 3 of 3 | 3 | |||||
STK3 | ENST00000649151.1 | n.427+6090G>A | intron_variant | Intron 3 of 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000374 AC: 9AN: 240832Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130696
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1456460Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 724010
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.58C>T (p.R20C) alteration is located in exon 2 (coding exon 1) of the KCNS2 gene. This alteration results from a C to T substitution at nucleotide position 58, causing the arginine (R) at amino acid position 20 to be replaced by a cysteine (C). 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