9-135784482-GCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC-GCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC

Variant summary

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

The NM_020822.3(KCNT1):c.2944-14_2944-7dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0052 (0 hom., cov: 0)
  • Exomes 𝑓: 0.011 (16 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNT1 NM_020822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

KCNT1 (HGNC:18865): (potassium sodium-activated channel subfamily T member 1) 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. This gene encodes a sodium-activated potassium channel subunit which is thought to function in ion conductance and developmental signaling pathways. Mutations in this gene cause the early-onset epileptic disorders, malignant migrating partial seizures of infancy and autosomal dominant nocturnal frontal lobe epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNT1	NM_020822.3	c.2944-14_2944-7dup		intron_variant		ENST00000371757.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNT1	ENST00000371757.7	c.2944-14_2944-7dup		intron_variant		1	NM_020822.3	A2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 352 AN: 67664 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00492

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00608

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00571

Gnomad SAS AF: 0.00589

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0154

Gnomad NFE AF: 0.00416

Gnomad OTH AF: 0.00225

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0111 AC: 4327 AN: 391482 Hom.: 16 Cov.: 0 AF XY: 0.0105 AC XY: 2193 AN XY: 208040

Gnomad4 AFR exome AF: 0.0148

Gnomad4 AMR exome AF: 0.00560

Gnomad4 ASJ exome AF: 0.0142

Gnomad4 EAS exome AF: 0.0133

Gnomad4 SAS exome AF: 0.00219

Gnomad4 FIN exome AF: 0.0116

Gnomad4 NFE exome AF: 0.0126

Gnomad4 OTH exome AF: 0.0130

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00515 AC: 349 AN: 67724 Hom.: 0 Cov.: 0 AF XY: 0.00615 AC XY: 193 AN XY: 31372

Gnomad4 AFR AF: 0.00496

Gnomad4 AMR AF: 0.00593

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.00531

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.00413

Gnomad4 OTH AF: 0.00223

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: rs55843930; hg19: chr9-138676328;