rs1962539

Variant names:

• chr2-18054345-C-A
• rs1962539
• ENST00000465292.5:n.306-116045C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-18054345-C-A
• chr2-18054345-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000465292.5(KCNS3):​n.306-116045C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,972 control chromosomes in the GnomAD database, including 17,585 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 0.47 (17585 hom., cov: 32)
• Consequence: KCNS3 ENST00000465292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 2 publications found

Genes affected

KCNS3 (HGNC:6302): (potassium voltage-gated channel modifier subfamily S member 3) 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. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465292.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNS3	ENST00000465292.5	TSL:4	n.306-116045C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70811 AN: 151852 Hom.: 17545 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.427

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.467 AC: 70902 AN: 151972 Hom.: 17585 Cov.: 32 AF XY: 0.465 AC XY: 34548 AN XY: 74286

African (AFR) AF: 0.640 AC: 26495 AN: 41430

American (AMR) AF: 0.472 AC: 7201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2319 AN: 5154

South Asian (SAS) AF: 0.490 AC: 2359 AN: 4810

European-Finnish (FIN) AF: 0.353 AC: 3723 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25930 AN: 67970

Other (OTH) AF: 0.432 AC: 913 AN: 2112

Alfa AF: 0.381 Hom.: 5547

Bravo AF: 0.481

Asia WGS AF: 0.480 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.51
PhyloP100		-2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1962539; hg19: chr2-18235611;