chr8-72839285-G-A

Position:

• chr8-72839285-G-A

Variant summary

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

The NM_004770.3(KCNB2):​c.580-96650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,150 control chromosomes in the GnomAD database, including 56,310 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 0.85 (56310 hom., cov: 32)
• Consequence: KCNB2 NM_004770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNB2	NM_004770.3	c.580-96650G>A		intron_variant		ENST00000523207.2	NP_004761.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNB2	ENST00000523207.2	c.580-96650G>A		intron_variant		1	NM_004770.3	ENSP00000430846	P1

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129708 AN: 152036 Hom.: 56291 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.853 AC: 129780 AN: 152150 Hom.: 56310 Cov.: 32 AF XY: 0.849 AC XY: 63139 AN XY: 74394

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.875

Alfa AF: 0.895 Hom.: 7636

Bravo AF: 0.843

Asia WGS AF: 0.704 AC: 2446 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.38

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: rs6983627; hg19: chr8-73751520;