chr2-17933665-C-T

Variant names:

• chr2-17933665-C-T
• rs1031771
• ENST00000465292.5:n.305+15794C>T

Variant summary

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

The ENST00000465292.5(KCNS3):​n.305+15794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,076 control chromosomes in the GnomAD database, including 6,951 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 0.29 (6951 hom., cov: 33)
• Consequence: KCNS3 ENST00000465292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNS3	ENST00000465292.5	TSL:4	n.305+15794C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43927 AN: 151958 Hom.: 6957 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.289 AC: 43913 AN: 152076 Hom.: 6951 Cov.: 33 AF XY: 0.288 AC XY: 21379 AN XY: 74324

African (AFR) AF: 0.153 AC: 6362 AN: 41500

American (AMR) AF: 0.293 AC: 4480 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1964 AN: 5166

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4822

European-Finnish (FIN) AF: 0.296 AC: 3125 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24236 AN: 67962

Other (OTH) AF: 0.312 AC: 661 AN: 2116

Alfa AF: 0.289 Hom.: 1231

Bravo AF: 0.284

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.48
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs1031771; hg19: chr2-18114932; COSMIC: COSV58406780;