rs4900026

Variant names:

• chr14-90162290-G-A
• rs4900026
• NM_022054.4:c.335-21821G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-90162290-G-A
• chr14-90162290-G-C

Variant summary

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

The NM_022054.4(KCNK13):​c.335-21821G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,094 control chromosomes in the GnomAD database, including 27,827 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 0.59 (27827 hom., cov: 33)
• Consequence: KCNK13 NM_022054.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 publications found

Genes affected

KCNK13 (HGNC:6275): (potassium two pore domain channel subfamily K member 13) Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a potassium channel containing two pore-forming domains. This protein is an open channel that can be stimulated by arachidonic acid and inhibited by the anesthetic halothane. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022054.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNK13	NM_022054.4	MANE Select	c.335-21821G>A		intron	N/A	NP_071337.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNK13	ENST00000282146.5	TSL:1 MANE Select	c.335-21821G>A		intron	N/A	ENSP00000282146.4
	KCNK13	ENST00000954166.1		c.380-21821G>A		intron	N/A	ENSP00000624225.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89928 AN: 151976 Hom.: 27826 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.591 AC: 89960 AN: 152094 Hom.: 27827 Cov.: 33 AF XY: 0.588 AC XY: 43705 AN XY: 74358

African (AFR) AF: 0.406 AC: 16814 AN: 41448

American (AMR) AF: 0.555 AC: 8486 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2321 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3344 AN: 5180

South Asian (SAS) AF: 0.534 AC: 2578 AN: 4824

European-Finnish (FIN) AF: 0.638 AC: 6753 AN: 10582

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47524 AN: 67984

Other (OTH) AF: 0.607 AC: 1282 AN: 2112

Alfa AF: 0.669 Hom.: 69584

Bravo AF: 0.578

Asia WGS AF: 0.533 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.59
PhyloP100		-1.4
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: rs4900026; hg19: chr14-90628634;