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GeneBe

22-38446037-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152868.3(KCNJ4):c.-40+8943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,118 control chromosomes in the GnomAD database, including 37,859 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 0.70 ( 37859 hom., cov: 32)

Consequence

KCNJ4
NM_152868.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.421
Variant links:
Genes affected
KCNJ4 (HGNC:6265): (potassium inwardly rectifying channel subfamily J member 4) Several different potassium channels are known to be involved with electrical signaling in the nervous system. One class is activated by depolarization whereas a second class is not. The latter are referred to as inwardly rectifying K+ channels, and they have a greater tendency to allow potassium to flow into the cell rather than out of it. This asymmetry in potassium ion conductance plays a key role in the excitability of muscle cells and neurons. The protein encoded by this gene is an integral membrane protein and member of the inward rectifier potassium channel family. The encoded protein has a small unitary conductance compared to other members of this protein family. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNJ4NM_152868.3 linkuse as main transcriptc.-40+8943A>G intron_variant ENST00000303592.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNJ4ENST00000303592.3 linkuse as main transcriptc.-40+8943A>G intron_variant 1 NM_152868.3 P1

Frequencies

GnomAD3 genomes
AF:
0.698
AC:
106107
AN:
152000
Hom.:
37804
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.805
Gnomad AMI
AF:
0.587
Gnomad AMR
AF:
0.676
Gnomad ASJ
AF:
0.637
Gnomad EAS
AF:
0.934
Gnomad SAS
AF:
0.877
Gnomad FIN
AF:
0.673
Gnomad MID
AF:
0.633
Gnomad NFE
AF:
0.616
Gnomad OTH
AF:
0.697
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.698
AC:
106218
AN:
152118
Hom.:
37859
Cov.:
32
AF XY:
0.705
AC XY:
52401
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.805
Gnomad4 AMR
AF:
0.676
Gnomad4 ASJ
AF:
0.637
Gnomad4 EAS
AF:
0.934
Gnomad4 SAS
AF:
0.877
Gnomad4 FIN
AF:
0.673
Gnomad4 NFE
AF:
0.616
Gnomad4 OTH
AF:
0.701
Alfa
AF:
0.656
Hom.:
7352
Bravo
AF:
0.700
Asia WGS
AF:
0.905
AC:
3147
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
6.3
Dann
Benign
0.39

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs196084; hg19: chr22-38842042; API