rs857978

Variant summary

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

The NM_002240.5(KCNJ6):​c.947-340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,260 control chromosomes in the GnomAD database, including 37,894 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 ( 37894 hom., cov: 35)

Consequence

KCNJ6
NM_002240.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140
Variant links:
Genes affected
KCNJ6 (HGNC:6267): (potassium inwardly rectifying channel subfamily J member 6) This gene encodes a member of the G protein-coupled inwardly-rectifying potassium channel family of inward rectifier potassium channels. This type of potassium channel allows a greater flow of potassium into the cell than out of it. These proteins modulate many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells, through G-protein coupled receptor stimulation. Mutations in this gene are associated with Keppen-Lubinsky Syndrome, a rare condition characterized by severe developmental delay, facial dysmorphism, and intellectual disability. [provided by RefSeq, Apr 2015]

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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNJ6NM_002240.5 linkuse as main transcriptc.947-340T>C intron_variant ENST00000609713.2 NP_002231.1 P48051
KCNJ6-AS1NR_183540.1 linkuse as main transcriptn.408-72731A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNJ6ENST00000609713.2 linkuse as main transcriptc.947-340T>C intron_variant 1 NM_002240.5 ENSP00000477437.1 P48051
KCNJ6ENST00000645093.1 linkuse as main transcriptc.947-340T>C intron_variant ENSP00000493772.1 P48051
ENSG00000286717ENST00000667151.1 linkuse as main transcriptn.161-20723A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.703
AC:
107014
AN:
152142
Hom.:
37871
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.744
Gnomad AMI
AF:
0.493
Gnomad AMR
AF:
0.756
Gnomad ASJ
AF:
0.680
Gnomad EAS
AF:
0.802
Gnomad SAS
AF:
0.650
Gnomad FIN
AF:
0.634
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.678
Gnomad OTH
AF:
0.699
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.703
AC:
107080
AN:
152260
Hom.:
37894
Cov.:
35
AF XY:
0.702
AC XY:
52274
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.744
Gnomad4 AMR
AF:
0.756
Gnomad4 ASJ
AF:
0.680
Gnomad4 EAS
AF:
0.802
Gnomad4 SAS
AF:
0.649
Gnomad4 FIN
AF:
0.634
Gnomad4 NFE
AF:
0.678
Gnomad4 OTH
AF:
0.698
Alfa
AF:
0.679
Hom.:
46174
Bravo
AF:
0.713
Asia WGS
AF:
0.752
AC:
2612
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.6
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

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

Other links and lift over

dbSNP: rs857978; hg19: chr21-38998126; API