rs6670661

Variant summary

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

The NM_001017425.3(KCNK2):​c.964-7728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,072 control chromosomes in the GnomAD database, including 21,141 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 0.51 ( 21141 hom., cov: 32)

Consequence

KCNK2
NM_001017425.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650
Variant links:
Genes affected
KCNK2 (HGNC:6277): (potassium two pore domain channel subfamily K member 2) This gene encodes one of the members of the two-pore-domain background potassium channel protein family. This type of potassium channel is formed by two homodimers that create a channel that leaks potassium out of the cell to control resting membrane potential. The channel can be opened, however, by certain anesthetics, membrane stretching, intracellular acidosis, and heat. Three transcript variants encoding different isoforms 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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNK2NM_001017425.3 linkuse as main transcriptc.964-7728G>A intron_variant ENST00000444842.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNK2ENST00000444842.7 linkuse as main transcriptc.964-7728G>A intron_variant 1 NM_001017425.3 O95069-1

Frequencies

GnomAD3 genomes
AF:
0.510
AC:
77464
AN:
151954
Hom.:
21135
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.316
Gnomad AMI
AF:
0.684
Gnomad AMR
AF:
0.571
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.613
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.686
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.590
Gnomad OTH
AF:
0.494
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.510
AC:
77498
AN:
152072
Hom.:
21141
Cov.:
32
AF XY:
0.510
AC XY:
37953
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.316
Gnomad4 AMR
AF:
0.572
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.613
Gnomad4 SAS
AF:
0.341
Gnomad4 FIN
AF:
0.686
Gnomad4 NFE
AF:
0.590
Gnomad4 OTH
AF:
0.495
Alfa
AF:
0.541
Hom.:
2770
Bravo
AF:
0.495
Asia WGS
AF:
0.452
AC:
1575
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.29
DANN
Benign
0.17

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: rs6670661; hg19: chr1-215400443; API