NM_001017425.3:c.476-10779G>C

Variant names:

• chr1-215158420-G-C
• rs2363556
• NM_001017425.3:c.476-10779G>C

Variant summary

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

The NM_001017425.3(KCNK2):​c.476-10779G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,104 control chromosomes in the GnomAD database, including 45,286 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 0.77 (45286 hom., cov: 31)
• Consequence: KCNK2 NM_001017425.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNK2	NM_001017425.3	c.476-10779G>C		intron_variant	Intron 3 of 6	ENST00000444842.7	NP_001017425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNK2	ENST00000444842.7	c.476-10779G>C		intron_variant	Intron 3 of 6	1	NM_001017425.3	ENSP00000394033.2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116885 AN: 151986 Hom.: 45247 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.769 AC: 116975 AN: 152104 Hom.: 45286 Cov.: 31 AF XY: 0.764 AC XY: 56797 AN XY: 74348

African (AFR) AF: 0.786 AC: 32602 AN: 41478

American (AMR) AF: 0.700 AC: 10683 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3468 AN: 5152

South Asian (SAS) AF: 0.551 AC: 2654 AN: 4818

European-Finnish (FIN) AF: 0.860 AC: 9111 AN: 10594

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53464 AN: 68010

Other (OTH) AF: 0.734 AC: 1549 AN: 2110

Alfa AF: 0.788 Hom.: 5861

Bravo AF: 0.764

Asia WGS AF: 0.613 AC: 2132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.72
PhyloP100		-0.20
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: rs2363556; hg19: chr1-215331763;