2-154761814-A-G

Variant summary

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

The NM_002239.4(KCNJ3):c.919+51995A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,000 control chromosomes in the GnomAD database, including 16,325 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 0.46 (16325 hom., cov: 32)
• Consequence: KCNJ3 NM_002239.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ3	NM_002239.4	c.919+51995A>G		intron_variant		ENST00000295101.3
KCNJ3	NM_001260508.2	c.702+62337A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ3	ENST00000295101.3	c.919+51995A>G		intron_variant		1	NM_002239.4	P1
KCNJ3	ENST00000544049.2	c.702+62337A>G		intron_variant		1
KCNJ3	ENST00000651198.1	c.382+51995A>G		intron_variant
KCNJ3	ENST00000493505.1	n.262+51995A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70284 AN: 151884 Hom.: 16312 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.463 AC: 70328 AN: 152000 Hom.: 16325 Cov.: 32 AF XY: 0.461 AC XY: 34281 AN XY: 74296

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.436

Alfa AF: 0.460 Hom.: 32289

Bravo AF: 0.454

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.69

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: rs2961957; hg19: chr2-155618326;