NM_005472.5:c.*1077_*1096dupATATATATATATATATATAT

Variant names:

• chr11-74456155-A-AATATATATATATATATATAT
• rs113583236
• NM_005472.5:c.*1077_*1096dupATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_005472.5(KCNE3):​c.*1077_*1096dupATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.028 (99 hom., cov: 0)
• Consequence: KCNE3 NM_005472.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

Genes affected

KCNE3 (HGNC:6243): (potassium voltage-gated channel subfamily E regulatory subunit 3) Voltage-gated potassium (Kv) 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 member of the potassium channel, voltage-gated, isk-related subfamily. This member is a type I membrane protein, and a beta subunit that assembles with a potassium channel alpha-subunit to modulate the gating kinetics and enhance stability of the multimeric complex. This gene is prominently expressed in the kidney. A missense mutation in this gene is associated with hypokalemic periodic paralysis. [provided by RefSeq, Jul 2008]

ENSG00000254928 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0282 (3177/112554) while in subpopulation NFE AF= 0.0401 (2087/52022). AF 95% confidence interval is 0.0387. There are 99 homozygotes in gnomad4. There are 1401 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 3177 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNE3	NM_005472.5	c.*1077_*1096dupATATATATATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	ENST00000310128.9	NP_005463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNE3	ENST00000310128	c.*1077_*1096dupATATATATATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005472.5	ENSP00000310557.4
ENSG00000254928	ENST00000530510.1	n.425+389_425+408dupTATATATATATATATATATA		intron_variant	Intron 1 of 1	2
ENSG00000254631	ENST00000533008.1	n.155-28016_155-27997dupTATATATATATATATATATA		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 3180 AN: 112530 Hom.: 99 Cov.: 0

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0540

Gnomad AMR AF: 0.0211

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0161

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0135

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0230

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0282 AC: 3177 AN: 112554 Hom.: 99 Cov.: 0 AF XY: 0.0264 AC XY: 1401 AN XY: 53074

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0211

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113583236; hg19: chr11-74167200;