rs2469515

chr8-132137856-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_004519.4(KCNQ3):c.1700+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,610,908 control chromosomes in the GnomAD database, including 35,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.17 (2567 hom., cov: 32)
  • Exomes 𝑓: 0.21 (32992 hom.)
• Consequence: KCNQ3 NM_004519.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.907

Genes affected

KCNQ3 (HGNC:6297): (potassium voltage-gated channel subfamily Q member 3) This gene encodes a protein that functions in the regulation of neuronal excitability. The encoded protein forms an M-channel by associating with the products of the related KCNQ2 or KCNQ5 genes, which both encode integral membrane proteins. M-channel currents are inhibited by M1 muscarinic acetylcholine receptors and are activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 2 (BFNC2), also known as epilepsy, benign neonatal type 2 (EBN2). Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 8-132137856-C-T is Benign according to our data. Variant chr8-132137856-C-T is described in ClinVar as [Benign]. Clinvar id is 670883.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-132137856-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNQ3	NM_004519.4	c.1700+29G>A		intron_variant		ENST00000388996.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNQ3	ENST00000388996.10	c.1700+29G>A		intron_variant		1	NM_004519.4	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25425 AN: 152088 Hom.: 2565 Cov.: 32

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.198

GnomAD3 exomes AF: 0.169 AC: 42367 AN: 250910 Hom.: 4391 AF XY: 0.176 AC XY: 23820 AN XY: 135678

Gnomad AFR exome AF: 0.0812

Gnomad AMR exome AF: 0.113

Gnomad ASJ exome AF: 0.216

Gnomad EAS exome AF: 0.00832

Gnomad SAS exome AF: 0.151

Gnomad FIN exome AF: 0.159

Gnomad NFE exome AF: 0.225

Gnomad OTH exome AF: 0.201

GnomAD4 exome AF: 0.205 AC: 299635 AN: 1458702 Hom.: 32992 Cov.: 32 AF XY: 0.205 AC XY: 149047 AN XY: 725854

Gnomad4 AFR exome AF: 0.0805

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.00867

Gnomad4 SAS exome AF: 0.155

Gnomad4 FIN exome AF: 0.159

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.167 AC: 25422 AN: 152206 Hom.: 2567 Cov.: 32 AF XY: 0.164 AC XY: 12184 AN XY: 74420

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.196

Alfa AF: 0.219 Hom.: 5354

Bravo AF: 0.163

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Seizures, benign familial neonatal, 2 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 19, 2021

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.65
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2469515; hg19: chr8-133150103;