rs1556905

Variant names:

• chr1-215188249-C-A
• rs1556905
• NM_001017425.3:c.824-6704C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-215188249-C-A
• chr1-215188249-C-G
• chr1-215188249-C-T

Variant summary

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

The NM_001017425.3(KCNK2):​c.824-6704C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,012 control chromosomes in the GnomAD database, including 10,815 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 0.37 (10815 hom., cov: 33)
• Consequence: KCNK2 NM_001017425.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNK2	NM_001017425.3	c.824-6704C>A		intron_variant	Intron 5 of 6	ENST00000444842.7	NP_001017425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNK2	ENST00000444842.7	c.824-6704C>A		intron_variant	Intron 5 of 6	1	NM_001017425.3	ENSP00000394033.2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56163 AN: 151894 Hom.: 10811 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.370 AC: 56184 AN: 152012 Hom.: 10815 Cov.: 33 AF XY: 0.372 AC XY: 27600 AN XY: 74290

African (AFR) AF: 0.280 AC: 11631 AN: 41472

American (AMR) AF: 0.396 AC: 6054 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1729 AN: 5146

South Asian (SAS) AF: 0.615 AC: 2965 AN: 4822

European-Finnish (FIN) AF: 0.330 AC: 3486 AN: 10558

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27174 AN: 67968

Other (OTH) AF: 0.430 AC: 905 AN: 2106

Alfa AF: 0.408 Hom.: 22010

Bravo AF: 0.365

Asia WGS AF: 0.465 AC: 1615 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.015
DANN	Benign	0.29
PhyloP100		-2.4
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: rs1556905; hg19: chr1-215361592;