rs653070

Positions:

• chr20-49470871-C-T

Variant summary

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

The NM_004975.4(KCNB1):​c.567+11043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,034 control chromosomes in the GnomAD database, including 31,421 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 0.64 (31421 hom., cov: 32)
• Consequence: KCNB1 NM_004975.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962

Genes affected

KCNB1 (HGNC:6231): (potassium voltage-gated channel subfamily B member 1) 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 and its activity is modulated by some other family members. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -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 = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNB1	NM_004975.4	c.567+11043G>A		intron_variant		ENST00000371741.6	NP_004966.1
KCNB1	XM_011528799.3	c.567+11043G>A		intron_variant			XP_011527101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNB1	ENST00000371741.6	c.567+11043G>A		intron_variant		1	NM_004975.4	ENSP00000360806	P1
KCNB1	ENST00000635465.1	c.567+11043G>A		intron_variant		1		ENSP00000489193	P1
KCNB1	ENST00000635878.1	c.96+11043G>A		intron_variant		5		ENSP00000489908
KCNB1	ENST00000636950.1	n.87+11043G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96711 AN: 151916 Hom.: 31380 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.637 AC: 96799 AN: 152034 Hom.: 31421 Cov.: 32 AF XY: 0.633 AC XY: 47074 AN XY: 74326

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.661

Alfa AF: 0.628 Hom.: 7129

Bravo AF: 0.631

Asia WGS AF: 0.489 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.20

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: rs653070; hg19: chr20-48087408;