NM_002239.4:c.920-57681T>A

Variant names:

• chr2-154797046-T-A
• rs1445654
• NM_002239.4:c.920-57681T>A

Variant summary

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

The NM_002239.4(KCNJ3):​c.920-57681T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,986 control chromosomes in the GnomAD database, including 44,302 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 0.76 (44302 hom., cov: 30)
• Consequence: KCNJ3 NM_002239.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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.920-57681T>A		intron	N/A	NP_002230.1
	KCNJ3	NM_001260508.2		c.703-57681T>A		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.920-57681T>A		intron	N/A	ENSP00000295101.2
	KCNJ3	ENST00000544049.2	TSL:1	c.703-57681T>A		intron	N/A	ENSP00000438410.1
	KCNJ3	ENST00000651198.1		c.383-57681T>A		intron	N/A	ENSP00000498639.1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114834 AN: 151868 Hom.: 44266 Cov.: 30

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.756 AC: 114924 AN: 151986 Hom.: 44302 Cov.: 30 AF XY: 0.758 AC XY: 56297 AN XY: 74268

African (AFR) AF: 0.591 AC: 24487 AN: 41414

American (AMR) AF: 0.768 AC: 11698 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2691 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4602 AN: 5142

South Asian (SAS) AF: 0.786 AC: 3783 AN: 4814

European-Finnish (FIN) AF: 0.860 AC: 9109 AN: 10594

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55973 AN: 67992

Other (OTH) AF: 0.780 AC: 1648 AN: 2112

Alfa AF: 0.783 Hom.: 5853

Bravo AF: 0.743

Asia WGS AF: 0.822 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.32
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: rs1445654; hg19: chr2-155653558;