chr18-79848203-C-G

Variant names:

• chr18-79848203-C-G
• rs4799092
• NM_012283.2:c.-114-8176C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012283.2(KCNG2):​c.-114-8176C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,058 control chromosomes in the GnomAD database, including 7,801 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 (7801 hom., cov: 33)
• Consequence: KCNG2 NM_012283.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012283.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNG2	NM_012283.2	MANE Select	c.-114-8176C>G		intron	N/A	NP_036415.1	Q9UJ96

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNG2	ENST00000316249.4	TSL:1 MANE Select	c.-114-8176C>G		intron	N/A	ENSP00000315654.3	Q9UJ96
	KCNG2	ENST00000958293.1		c.-140-8150C>G		intron	N/A	ENSP00000628352.1
	KCNG2	ENST00000958294.1		c.-40-15425C>G		intron	N/A	ENSP00000628353.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45561 AN: 151942 Hom.: 7799 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.300 AC: 45569 AN: 152058 Hom.: 7801 Cov.: 33 AF XY: 0.302 AC XY: 22455 AN XY: 74326

African (AFR) AF: 0.139 AC: 5767 AN: 41498

American (AMR) AF: 0.394 AC: 6019 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2215 AN: 5146

South Asian (SAS) AF: 0.518 AC: 2498 AN: 4822

European-Finnish (FIN) AF: 0.285 AC: 3011 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23881 AN: 67966

Other (OTH) AF: 0.289 AC: 609 AN: 2104

Alfa AF: 0.184 Hom.: 403

Bravo AF: 0.302

Asia WGS AF: 0.481 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.40
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4799092; hg19: chr18-77608203;