rs7236339

Positions:

• chr18-79819773-G-A

Variant summary

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

The NM_012283.2(KCNG2):​c.-115+21759G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,212 control chromosomes in the GnomAD database, including 2,872 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 0.19 (2872 hom., cov: 33)
• Consequence: KCNG2 NM_012283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

Genes affected

KCNG2 (HGNC:6249): (potassium voltage-gated channel modifier subfamily G 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. This gene encodes a member of the potassium channel, voltage-gated, subfamily G. This member is a gamma subunit of the voltage-gated potassium channel. The delayed-rectifier type channels containing this subunit may contribute to cardiac action potential repolarization. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNG2	NM_012283.2	c.-115+21759G>A		intron_variant		ENST00000316249.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNG2	ENST00000316249.4	c.-115+21759G>A		intron_variant		1	NM_012283.2	P1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29246 AN: 152094 Hom.: 2871 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.192 AC: 29271 AN: 152212 Hom.: 2872 Cov.: 33 AF XY: 0.190 AC XY: 14107 AN XY: 74422

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.190

Alfa AF: 0.203 Hom.: 6816

Bravo AF: 0.186

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7236339; hg19: chr18-77579773;