rs540783

chr10-77317955-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161352.2(KCNMA1):c.541-66699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,110 control chromosomes in the GnomAD database, including 3,510 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 0.21 (3510 hom., cov: 32)
• Consequence: KCNMA1 NM_001161352.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNMA1	NM_001161352.2	c.541-66699G>A		intron_variant		ENST00000286628.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNMA1	ENST00000286628.14	c.541-66699G>A		intron_variant		1	NM_001161352.2	A2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31458 AN: 151992 Hom.: 3503 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.224

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31495 AN: 152110 Hom.: 3510 Cov.: 32 AF XY: 0.208 AC XY: 15441 AN XY: 74326

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.226

Alfa AF: 0.212 Hom.: 1594

Bravo AF: 0.207

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.8
Dann	Benign	0.70

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

Other links and lift over

dbSNP: rs540783; hg19: chr10-79077713;