rs2383869

Positions:

• chr8-72654226-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004770.3(KCNB2):​c.579+85913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,076 control chromosomes in the GnomAD database, including 14,188 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 0.40 (14188 hom., cov: 32)
• Consequence: KCNB2 NM_004770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

KCNB2 (HGNC:6232): (potassium voltage-gated channel subfamily B member 2) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shab-related subfamily. This member is a delayed rectifier potassium channel. The gene is expressed in gastrointestinal smooth muscle cells. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNB2	NM_004770.3	c.579+85913C>T		intron_variant		ENST00000523207.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNB2	ENST00000523207.2	c.579+85913C>T		intron_variant		1	NM_004770.3	P1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61484 AN: 151958 Hom.: 14181 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.405 AC: 61519 AN: 152076 Hom.: 14188 Cov.: 32 AF XY: 0.401 AC XY: 29829 AN XY: 74318

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.416

Alfa AF: 0.476 Hom.: 11255

Bravo AF: 0.401

Asia WGS AF: 0.288 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.71

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: rs2383869; hg19: chr8-73566461;