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GeneBe

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20
Variant links:
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
KCNN3NM_002249.6 linkuse as main transcriptc.933+9204A>G intron_variant ENST00000271915.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNN3ENST00000361147.8 linkuse as main transcriptc.-116A>G 5_prime_UTR_variant 1/81 Q9UGI6-2
KCNN3ENST00000271915.9 linkuse as main transcriptc.933+9204A>G intron_variant 1 NM_002249.6 P1Q9UGI6-1
KCNN3ENST00000358505.2 linkuse as main transcriptc.-7+8121A>G intron_variant 1 Q9UGI6-3
KCNN3ENST00000618040.4 linkuse as main transcriptc.933+9204A>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.656
AC:
99787
AN:
152090
Hom.:
34459
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.440
Gnomad AMI
AF:
0.595
Gnomad AMR
AF:
0.750
Gnomad ASJ
AF:
0.631
Gnomad EAS
AF:
0.990
Gnomad SAS
AF:
0.807
Gnomad FIN
AF:
0.757
Gnomad MID
AF:
0.656
Gnomad NFE
AF:
0.716
Gnomad OTH
AF:
0.671
GnomAD4 exome
AF:
0.727
AC:
1058903
AN:
1457040
Hom.:
388998
Cov.:
35
AF XY:
0.729
AC XY:
528072
AN XY:
724616
show subpopulations
Gnomad4 AFR exome
AF:
0.424
Gnomad4 AMR exome
AF:
0.825
Gnomad4 ASJ exome
AF:
0.654
Gnomad4 EAS exome
AF:
0.994
Gnomad4 SAS exome
AF:
0.798
Gnomad4 FIN exome
AF:
0.756
Gnomad4 NFE exome
AF:
0.718
Gnomad4 OTH exome
AF:
0.716
GnomAD4 genome
AF:
0.656
AC:
99858
AN:
152208
Hom.:
34481
Cov.:
34
AF XY:
0.667
AC XY:
49635
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.440
Gnomad4 AMR
AF:
0.750
Gnomad4 ASJ
AF:
0.631
Gnomad4 EAS
AF:
0.990
Gnomad4 SAS
AF:
0.807
Gnomad4 FIN
AF:
0.757
Gnomad4 NFE
AF:
0.716
Gnomad4 OTH
AF:
0.674
Alfa
AF:
0.703
Hom.:
18237
Bravo
AF:
0.648
Asia WGS
AF:
0.886
AC:
3077
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
0.45
Dann
Benign
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4845397; hg19: chr1-154832304; API