rs760628050

chr10-77637586-TCCGCCGCCGCCGCCG-Tchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGCCGCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGCCGCCGCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGCCGCCGCCGCCGCCGchr10-77637586-TCCGCCGCCGCCGCCG-TCCGCCGCCGCCGCCGCCGCCGCCGCCG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001161352.2(KCNMA1):c.42_56del(p.Gly16_Gly20del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KCNMA1 NM_001161352.2 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.59

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNMA1	NM_001161352.2	c.42_56del	p.Gly16_Gly20del	inframe_deletion	1/28	ENST00000286628.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNMA1	ENST00000286628.14	c.42_56del	p.Gly16_Gly20del	inframe_deletion	1/28	1	NM_001161352.2	A2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs760628050; hg19: chr10-79397344;