Variant rs2306799 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002250.3(KCNN4):c.820-60C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,173,166 control chromosomes in the GnomAD database, including 22,746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3152 hom., cov: 31)

Exomes 𝑓: 0.19 ( 19594 hom. )

Consequence

KCNN4
NM_002250.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.884

Variant links:

Genes affected

KCNN4 (HGNC:6293): (potassium calcium-activated channel subfamily N member 4) The protein encoded by this gene is part of a potentially heterotetrameric voltage-independent potassium channel that is activated by intracellular calcium. Activation is followed by membrane hyperpolarization, which promotes calcium influx. The encoded protein may be part of the predominant calcium-activated potassium channel in T-lymphocytes. This gene is similar to other KCNN family potassium channel genes, but it differs enough to possibly be considered as part of a new subfamily. [provided by RefSeq, Jul 2008]

KCNN4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 19-43769889-G-A is Benign according to our data. Variant chr19-43769889-G-A is described in ClinVar as [Benign]. Clinvar id is 1283590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNN4	NM_002250.3 linkuse as main transcript	c.820-60C>T		intron_variant		ENST00000648319.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNN4	ENST00000648319.1 linkuse as main transcript	c.820-60C>T		intron_variant			NM_002250.3	P1

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30650

AN:

151734

Hom.:

3155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.214

GnomAD4 exome

AF:

0.193

AC:

196614

AN:

1021316

Hom.:

19594

AF XY:

0.192

AC XY:

100019

AN XY:

521680

show subpopulations

Gnomad4 AFR exome

AF:

0.211

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.228

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.157

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.202

AC:

30645

AN:

151850

Hom.:

3152

Cov.:

AF XY:

0.200

AC XY:

14825

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.132

Hom.:

362

Bravo

AF:

0.199

Asia WGS

AF:

0.201

AC:

697

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.29

DANN

Benign

0.64

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