NM_021614.4:c.428_439delACGCGCAGCAGT
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_021614.4(KCNN2):c.428_439delACGCGCAGCAGT(p.Tyr143_Gln146del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000391 in 460,938 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
KCNN2
NM_021614.4 disruptive_inframe_deletion
NM_021614.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.06
Genes affected
KCNN2 (HGNC:6291): (potassium calcium-activated channel subfamily N member 2) Action potentials in vertebrate neurons are followed by an afterhyperpolarization (AHP) that may persist for several seconds and may have profound consequences for the firing pattern of the neuron. Each component of the AHP is kinetically distinct and is mediated by different calcium-activated potassium channels. The protein encoded by this gene is activated before membrane hyperpolarization and is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene is a member of the KCNN family of potassium channel genes. The encoded protein is an integral membrane protein that forms a voltage-independent calcium-activated channel with three other calmodulin-binding subunits. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_021614.4.
BS2
High AC in GnomAdExome4 at 18 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCNN2 | ENST00000673685.1 | c.428_439delACGCGCAGCAGT | p.Tyr143_Gln146del | disruptive_inframe_deletion | Exon 1 of 8 | NM_021614.4 | ENSP00000501239.1 | |||
KCNN2 | ENST00000512097.10 | c.626_637delACGCGCAGCAGT | p.Tyr209_Gln212del | disruptive_inframe_deletion | Exon 6 of 13 | 5 | ENSP00000427120.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.0000391 AC: 18AN: 460938Hom.: 0 AF XY: 0.0000292 AC XY: 7AN XY: 239774
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GnomAD4 genome Cov.: 33
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33
Bravo
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at