rs12131478

chr1-215013629-G-Achr1-215013629-G-T

Variant summary

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

The ENST00000391895.6(KCNK2):c.34+7674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,858 control chromosomes in the GnomAD database, including 6,885 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 0.29 (6885 hom., cov: 32)
• Consequence: KCNK2 ENST00000391895.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNK2	NM_001017424.3	c.34+7674G>A		intron_variant
KCNK2	XM_017001249.2	c.-85+7674G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNK2	ENST00000391895.6	c.34+7674G>A		intron_variant		1
KCNK2	ENST00000467031.5	c.34+7674G>A		intron_variant, NMD_transcript_variant		1
KCNK2	ENST00000486921.5	c.34+7674G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44107 AN: 151740 Hom.: 6884 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.291 AC: 44129 AN: 151858 Hom.: 6885 Cov.: 32 AF XY: 0.297 AC XY: 22012 AN XY: 74172

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.309

Alfa AF: 0.309 Hom.: 12115

Bravo AF: 0.292

Asia WGS AF: 0.434 AC: 1500 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.5
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12131478; hg19: chr1-215186972;