rs4900022

Variant names:

• chr14-90149169-G-A
• rs4900022
• NM_022054.4:c.335-34942G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-90149169-G-A
• chr14-90149169-G-C
• chr14-90149169-G-T

Variant summary

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

The NM_022054.4(KCNK13):​c.335-34942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,184 control chromosomes in the GnomAD database, including 70,490 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 0.96 (70490 hom., cov: 30)
• Consequence: KCNK13 NM_022054.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 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.335-34942G>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.335-34942G>A		intron	N/A	ENSP00000282146.4	Q9HB14
	KCNK13	ENST00000954166.1		c.379+14406G>A		intron	N/A	ENSP00000624225.1

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146306 AN: 152066 Hom.: 70462 Cov.: 30

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.962 AC: 146384 AN: 152184 Hom.: 70490 Cov.: 30 AF XY: 0.963 AC XY: 71667 AN XY: 74390

African (AFR) AF: 0.907 AC: 37628 AN: 41492

American (AMR) AF: 0.976 AC: 14916 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3428 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5038 AN: 5154

South Asian (SAS) AF: 0.980 AC: 4727 AN: 4822

European-Finnish (FIN) AF: 0.995 AC: 10555 AN: 10604

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66876 AN: 68032

Other (OTH) AF: 0.963 AC: 2036 AN: 2114

Alfa AF: 0.977 Hom.: 3747

Bravo AF: 0.958

Asia WGS AF: 0.933 AC: 3244 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	3.4
DANN	Benign	0.35
PhyloP100		-0.83
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: rs4900022; hg19: chr14-90615513;