chr11-74456155-A-AATATATATATAT

Variant names:

• chr11-74456155-A-AATATATATATAT
• rs113583236
• NM_005472.5:c.*1085_*1096dupATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_005472.5(KCNE3):​c.*1085_*1096dupATATATATATAT 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 0.046 (237 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNE3	NM_005472.5	c.*1085_*1096dupATATATATATAT		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.*1085_*1096dupATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005472.5	ENSP00000310557.4
ENSG00000254928	ENST00000530510.1	n.425+397_425+408dupTATATATATATA		intron_variant	Intron 1 of 1	2
ENSG00000254631	ENST00000533008.1	n.155-28008_155-27997dupTATATATATATA		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0457 AC: 5149 AN: 112682 Hom.: 237 Cov.: 0

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0319

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0500

Gnomad MID AF: 0.0270

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0407

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0457 AC: 5152 AN: 112706 Hom.: 237 Cov.: 0 AF XY: 0.0439 AC XY: 2332 AN XY: 53134

Gnomad4 AFR AF: 0.0364

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0319

Gnomad4 EAS AF: 0.0682

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0500

Gnomad4 NFE AF: 0.0560

Gnomad4 OTH AF: 0.0403

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;