Variant rs2616652 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001161352.2(KCNMA1):c.809-26648A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,210 control chromosomes in the GnomAD database, including 57,614 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 0.87 ( 57588 hom., cov: 31)

Exomes 𝑓: 0.81 ( 26 hom. )

Consequence

KCNMA1
NM_001161352.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.67

Variant links:

Genes affected

KCNMA1 (HGNC:6284): (potassium calcium-activated channel subfamily M alpha 1) This gene encodes the alpha subunit of calcium-activated BK channel. The encoded protein is involved in several physiological processes including smooth muscle contraction, neurotransmitter release and neuronal excitability. Mutations in this gene are associated with a spectrum of neurological disorders including Paroxysmal Nonkinesigenic Dyskinesia 3, Idiopathic Generalized Epilepsy 16 and Liang-Wang syndrome. [provided by RefSeq, Aug 2022]

KCNMA1 links:

KCNMA1-AS2 (HGNC:51214): (KCNMA1 antisense RNA 2)

KCNMA1-AS2 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=-0.58).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNMA1	NM_001161352.2 link	c.809-26648A>T		intron_variant		ENST00000286628.14	NP_001154824.1	Q12791-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNMA1	ENST00000286628.14 link	c.809-26648A>T		intron_variant		1	NM_001161352.2	ENSP00000286628.8		Q12791-1

Frequencies

GnomAD3 genomes

AF:

0.870

AC:

132256

AN:

152018

Hom.:

57543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.774

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.885

Gnomad EAS

AF:

0.915

Gnomad SAS

AF:

0.864

Gnomad FIN

AF:

0.838

Gnomad MID

AF:

0.883

Gnomad NFE

AF:

0.844

Gnomad OTH

AF:

0.871

GnomAD4 exome

AF:

0.811

AC:

AN:

Hom.:

Cov.:

AF XY:

0.794

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.833

Gnomad4 NFE exome

AF:

0.803

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.870

AC:

132357

AN:

152136

Hom.:

57588

Cov.:

AF XY:

0.871

AC XY:

64764

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.899

Gnomad4 AMR

AF:

0.915

Gnomad4 ASJ

AF:

0.885

Gnomad4 EAS

AF:

0.915

Gnomad4 SAS

AF:

0.864

Gnomad4 FIN

AF:

0.838

Gnomad4 NFE

AF:

0.844

Gnomad4 OTH

AF:

0.873

Alfa

AF:

0.852

Hom.:

6446

Bravo

AF:

0.878

Asia WGS

AF:

0.879

AC:

3056

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.72

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