rs13043825
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001322799.2(KCNS1):c.258G>A(p.Glu86=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,519,866 control chromosomes in the GnomAD database, including 50,129 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3807 hom., cov: 32)
Exomes 𝑓: 0.25 ( 46322 hom. )
Consequence
KCNS1
NM_001322799.2 synonymous
NM_001322799.2 synonymous
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.39
Genes affected
KCNS1 (HGNC:6300): (potassium voltage-gated channel modifier subfamily S member 1) Voltage-gated potassium channels form the largest and most diversified class of ion channels and are present in both excitable and nonexcitable cells. Their main functions are associated with the regulation of the resting membrane potential and the control of the shape and frequency of action potentials. The alpha subunits are of 2 types: those that are functional by themselves and those that are electrically silent but capable of modulating the activity of specific functional alpha subunits. The protein encoded by this gene is not functional by itself but can form heteromultimers with member 1 and with member 2 (and possibly other members) of the Shab-related subfamily of potassium voltage-gated channel proteins. This gene belongs to the S subfamily of the potassium channel family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
?
Synonymous conserved (PhyloP=2.39 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNS1 | NM_001322799.2 | c.258G>A | p.Glu86= | synonymous_variant | 3/4 | ENST00000537075.3 | |
KCNS1 | NM_002251.5 | c.258G>A | p.Glu86= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNS1 | ENST00000537075.3 | c.258G>A | p.Glu86= | synonymous_variant | 3/4 | 1 | NM_001322799.2 | P1 | |
KCNS1 | ENST00000306117.5 | c.258G>A | p.Glu86= | synonymous_variant | 4/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.198 AC: 29984AN: 151316Hom.: 3807 Cov.: 32
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GnomAD3 exomes AF: 0.224 AC: 26741AN: 119644Hom.: 3451 AF XY: 0.221 AC XY: 14451AN XY: 65486
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GnomAD4 exome AF: 0.253 AC: 345675AN: 1368440Hom.: 46322 Cov.: 34 AF XY: 0.250 AC XY: 168828AN XY: 674488
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GnomAD4 genome ? AF: 0.198 AC: 29974AN: 151426Hom.: 3807 Cov.: 32 AF XY: 0.201 AC XY: 14914AN XY: 74036
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at