Variant 1-110601828-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004974.4(KCNA2):c.*1455C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0161 in 1,235,860 control chromosomes in the GnomAD database, including 1,659 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.065 ( 1072 hom., cov: 27)

Exomes 𝑓: 0.0097 ( 587 hom. )

Consequence

KCNA2
NM_004974.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.312

Variant links:

Genes affected

KCNA2 (HGNC:6220): (potassium voltage-gated channel subfamily A member 2) 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. The coding region of this gene is intronless, and the gene is clustered with genes KCNA3 and KCNA10 on chromosome 1. [provided by RefSeq, Jul 2008]

KCNA2 links:

KCNA2 (HGNC:):

KCNA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 1-110601828-G-A is Benign according to our data. Variant chr1-110601828-G-A is described in ClinVar as [Benign]. Clinvar id is 1246346.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNA2	NM_004974.4 linkuse as main transcript	c.*1455C>T		3_prime_UTR_variant	3/3	ENST00000316361.10	NP_004965.1	P16389-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNA2	ENST00000316361 linkuse as main transcript	c.*1455C>T		3_prime_UTR_variant	3/3	2	NM_004974.4	ENSP00000314520.4		P16389-1

Frequencies

GnomAD3 genomes

AF:

0.0651

AC:

9329

AN:

143378

Hom.:

1066

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0273

Gnomad ASJ

AF:

0.00409

Gnomad EAS

AF:

0.00244

Gnomad SAS

AF:

0.00227

Gnomad FIN

AF:

0.000422

Gnomad MID

AF:

0.0390

Gnomad NFE

AF:

0.00187

Gnomad OTH

AF:

0.0501

GnomAD4 exome

AF:

0.00965

AC:

10545

AN:

1092408

Hom.:

587

Cov.:

AF XY:

0.00887

AC XY:

4648

AN XY:

524112

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.0236

Gnomad4 ASJ exome

AF:

0.00463

Gnomad4 EAS exome

AF:

0.00991

Gnomad4 SAS exome

AF:

0.00828

Gnomad4 FIN exome

AF:

0.00271

Gnomad4 NFE exome

AF:

0.00427

Gnomad4 OTH exome

AF:

0.0189

GnomAD4 genome

AF:

0.0652

AC:

9358

AN:

143452

Hom.:

1072

Cov.:

AF XY:

0.0633

AC XY:

4396

AN XY:

69460

show subpopulations

Gnomad4 AFR

AF:

0.228

Gnomad4 AMR

AF:

0.0273

Gnomad4 ASJ

AF:

0.00409

Gnomad4 EAS

AF:

0.00245

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.000422

Gnomad4 NFE

AF:

0.00187

Gnomad4 OTH

AF:

0.0497

Alfa

AF:

0.00125

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.33

DANN

Benign

0.16

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over