18-79832660-C-G

Position:

• chr18-79832660-C-G

Variant summary

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

The NM_012283.2(KCNG2):​c.-114-23719C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,122 control chromosomes in the GnomAD database, including 7,916 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 0.30 (7916 hom., cov: 33)
• Consequence: KCNG2 NM_012283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNG2	NM_012283.2	c.-114-23719C>G		intron_variant		ENST00000316249.4	NP_036415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNG2	ENST00000316249.4	c.-114-23719C>G		intron_variant		1	NM_012283.2	ENSP00000315654.3

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46019 AN: 152004 Hom.: 7913 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.303 AC: 46028 AN: 152122 Hom.: 7916 Cov.: 33 AF XY: 0.305 AC XY: 22681 AN XY: 74364

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.289

Alfa AF: 0.185 Hom.: 407

Bravo AF: 0.306

Asia WGS AF: 0.487 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs537962; hg19: chr18-77592660;