Variant rs1058184 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002232.5(KCNA3):c.*232T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 500,590 control chromosomes in the GnomAD database, including 113,828 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 0.67 ( 34209 hom., cov: 31)

Exomes 𝑓: 0.67 ( 79619 hom. )

Consequence

KCNA3
NM_002232.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.814

Variant links:

Genes affected

KCNA3 (HGNC:6221): (potassium voltage-gated channel subfamily A member 3) 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. Four sequence-related potassium channel genes - shaker, shaw, shab, and shal - have been identified in Drosophila, and each has been shown to have human homolog(s). This gene encodes a member of the potassium channel, voltage-gated, shaker-related subfamily. This member contains six membrane-spanning domains with a shaker-type repeat in the fourth segment. It belongs to the delayed rectifier class, members of which allow nerve cells to efficiently repolarize following an action potential. It plays an essential role in T-cell proliferation and activation. This gene appears to be intronless and it is clustered together with KCNA2 and KCNA10 genes on chromosome 1. [provided by RefSeq, Jul 2008]

KCNA3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNA3	NM_002232.5 linkuse as main transcript	c.*232T>G		3_prime_UTR_variant	1/1	ENST00000369769.4
KCNA3	NR_109845.2 linkuse as main transcript	n.218+387T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNA3	ENST00000369769.4 linkuse as main transcript	c.*232T>G		3_prime_UTR_variant	1/1		NM_002232.5	P1

Frequencies

GnomAD3 genomes

AF:

0.671

AC:

101797

AN:

151820

Hom.:

34189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.666

Gnomad AMI

AF:

0.569

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.555

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.687

GnomAD4 exome

AF:

0.671

AC:

233975

AN:

348648

Hom.:

79619

Cov.:

AF XY:

0.669

AC XY:

120949

AN XY:

180656

show subpopulations

Gnomad4 AFR exome

AF:

0.665

Gnomad4 AMR exome

AF:

0.648

Gnomad4 ASJ exome

AF:

0.753

Gnomad4 EAS exome

AF:

0.531

Gnomad4 SAS exome

AF:

0.577

Gnomad4 FIN exome

AF:

0.674

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.672

GnomAD4 genome

AF:

0.670

AC:

101862

AN:

151942

Hom.:

34209

Cov.:

AF XY:

0.664

AC XY:

49275

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.666

Gnomad4 AMR

AF:

0.643

Gnomad4 ASJ

AF:

0.737

Gnomad4 EAS

AF:

0.555

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.663

Gnomad4 NFE

AF:

0.694

Gnomad4 OTH

AF:

0.685

Alfa

AF:

0.695

Hom.:

60294

Bravo

AF:

0.669

Asia WGS

AF:

0.571

AC:

1987

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

4.9

DANN

Benign

0.54

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over