rs4845396
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002249.6(KCNN3):c.933+13099C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,022 control chromosomes in the GnomAD database, including 19,588 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 0.48 ( 19588 hom., cov: 31)
Consequence
KCNN3
NM_002249.6 intron
NM_002249.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0930
Genes affected
KCNN3 (HGNC:6292): (potassium calcium-activated channel subfamily N member 3) 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. This gene belongs to the KCNN family of potassium channels. It encodes an integral membrane protein that forms a voltage-independent calcium-activated channel, which is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene contains two CAG repeat regions in the coding sequence. It was thought that expansion of one or both of these repeats could lead to an increased susceptibility to schizophrenia or bipolar disorder, but studies indicate that this is probably not the case. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KCNN3 | ENST00000271915.9 | c.933+13099C>T | intron_variant | Intron 1 of 7 | 1 | NM_002249.6 | ENSP00000271915.3 | |||
| KCNN3 | ENST00000361147.8 | c.18+3762C>T | intron_variant | Intron 1 of 7 | 1 | ENSP00000354764.4 | ||||
| KCNN3 | ENST00000358505.2 | c.-7+12016C>T | intron_variant | Intron 1 of 7 | 1 | ENSP00000351295.2 | ||||
| KCNN3 | ENST00000618040.4 | c.933+13099C>T | intron_variant | Intron 1 of 8 | 5 | ENSP00000481848.1 |
Frequencies
GnomAD3 genomes 0.479 AC: 72690AN: 151904Hom.: 19573 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.478 AC: 72740AN: 152022Hom.: 19588 Cov.: 31 AF XY: 0.493 AC XY: 36597AN XY: 74304
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2791
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at