1-154859828-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000361147.8(KCNN3):c.-116A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 1,609,248 control chromosomes in the GnomAD database, including 423,479 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 0.66 ( 34481 hom., cov: 34)
Exomes 𝑓: 0.73 ( 388998 hom. )
Consequence
KCNN3
ENST00000361147.8 5_prime_UTR
ENST00000361147.8 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.20
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNN3 | NM_002249.6 | c.933+9204A>G | intron_variant | ENST00000271915.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNN3 | ENST00000361147.8 | c.-116A>G | 5_prime_UTR_variant | 1/8 | 1 | ||||
KCNN3 | ENST00000271915.9 | c.933+9204A>G | intron_variant | 1 | NM_002249.6 | P1 | |||
KCNN3 | ENST00000358505.2 | c.-7+8121A>G | intron_variant | 1 | |||||
KCNN3 | ENST00000618040.4 | c.933+9204A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.656 AC: 99787AN: 152090Hom.: 34459 Cov.: 34
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GnomAD4 exome AF: 0.727 AC: 1058903AN: 1457040Hom.: 388998 Cov.: 35 AF XY: 0.729 AC XY: 528072AN XY: 724616
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GnomAD4 genome ? AF: 0.656 AC: 99858AN: 152208Hom.: 34481 Cov.: 34 AF XY: 0.667 AC XY: 49635AN XY: 74428
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at