rs3106658

Variant names:

• chr2-154711550-T-C
• rs3106658
• NM_002239.4:c.919+1731T>C

Variant summary

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

The NM_002239.4(KCNJ3):​c.919+1731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,888 control chromosomes in the GnomAD database, including 22,082 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 0.53 (22082 hom., cov: 33)
• Consequence: KCNJ3 NM_002239.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 5 publications found

Genes affected

KCNJ3 (HGNC:6264): (potassium inwardly rectifying channel subfamily J member 3) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein, which has a greater tendency to allow potassium to flow into a cell rather than out of a cell, is controlled by G-proteins and plays an important role in regulating heartbeat. It associates with three other G-protein-activated potassium channels to form a heteromultimeric pore-forming complex that also couples to neurotransmitter receptors in the brain and whereby channel activation can inhibit action potential firing by hyperpolarizing the plasma membrane. These multimeric G-protein-gated inwardly-rectifying potassium (GIRK) channels may play a role in the pathophysiology of epilepsy, addiction, Down's syndrome, ataxia, and Parkinson's disease. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, May 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002239.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNJ3	NM_002239.4	MANE Select	c.919+1731T>C		intron	N/A	NP_002230.1
	KCNJ3	NM_001260508.2		c.702+12073T>C		intron	N/A	NP_001247437.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNJ3	ENST00000295101.3	TSL:1 MANE Select	c.919+1731T>C		intron	N/A	ENSP00000295101.2
	KCNJ3	ENST00000544049.2	TSL:1	c.702+12073T>C		intron	N/A	ENSP00000438410.1
	KCNJ3	ENST00000651198.1		c.382+1731T>C		intron	N/A	ENSP00000498639.1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80385 AN: 151768 Hom.: 22035 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.530 AC: 80483 AN: 151888 Hom.: 22082 Cov.: 33 AF XY: 0.530 AC XY: 39335 AN XY: 74220

African (AFR) AF: 0.674 AC: 27936 AN: 41446

American (AMR) AF: 0.435 AC: 6645 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2395 AN: 5152

South Asian (SAS) AF: 0.446 AC: 2153 AN: 4826

European-Finnish (FIN) AF: 0.578 AC: 6102 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32014 AN: 67854

Other (OTH) AF: 0.493 AC: 1041 AN: 2110

Alfa AF: 0.479 Hom.: 9345

Bravo AF: 0.528

Asia WGS AF: 0.490 AC: 1700 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.29
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3106658; hg19: chr2-155568062;