rs1061122

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000271915.9(KCNN3):​c.933+9218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,612,166 control chromosomes in the GnomAD database, including 42,768 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 0.27 ( 6422 hom., cov: 33)
Exomes 𝑓: 0.21 ( 36346 hom. )

Consequence

KCNN3
ENST00000271915.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.39
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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNN3NM_002249.6 linkuse as main transcriptc.933+9218G>A intron_variant ENST00000271915.9 NP_002240.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNN3ENST00000361147.8 linkuse as main transcriptc.-102G>A 5_prime_UTR_variant 1/81 ENSP00000354764 Q9UGI6-2
KCNN3ENST00000271915.9 linkuse as main transcriptc.933+9218G>A intron_variant 1 NM_002249.6 ENSP00000271915 P1Q9UGI6-1
KCNN3ENST00000358505.2 linkuse as main transcriptc.-7+8135G>A intron_variant 1 ENSP00000351295 Q9UGI6-3
KCNN3ENST00000618040.4 linkuse as main transcriptc.933+9218G>A intron_variant 5 ENSP00000481848

Frequencies

GnomAD3 genomes
AF:
0.268
AC:
40720
AN:
152052
Hom.:
6418
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.430
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.267
Gnomad EAS
AF:
0.00923
Gnomad SAS
AF:
0.127
Gnomad FIN
AF:
0.198
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.227
Gnomad OTH
AF:
0.241
GnomAD4 exome
AF:
0.214
AC:
313144
AN:
1459996
Hom.:
36346
Cov.:
32
AF XY:
0.212
AC XY:
153926
AN XY:
726312
show subpopulations
Gnomad4 AFR exome
AF:
0.436
Gnomad4 AMR exome
AF:
0.136
Gnomad4 ASJ exome
AF:
0.254
Gnomad4 EAS exome
AF:
0.00552
Gnomad4 SAS exome
AF:
0.132
Gnomad4 FIN exome
AF:
0.198
Gnomad4 NFE exome
AF:
0.225
Gnomad4 OTH exome
AF:
0.214
GnomAD4 genome
AF:
0.268
AC:
40745
AN:
152170
Hom.:
6422
Cov.:
33
AF XY:
0.259
AC XY:
19252
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.430
Gnomad4 AMR
AF:
0.191
Gnomad4 ASJ
AF:
0.267
Gnomad4 EAS
AF:
0.00963
Gnomad4 SAS
AF:
0.127
Gnomad4 FIN
AF:
0.198
Gnomad4 NFE
AF:
0.227
Gnomad4 OTH
AF:
0.238
Alfa
AF:
0.230
Hom.:
8847
Bravo
AF:
0.273
Asia WGS
AF:
0.0710
AC:
251
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.012
DANN
Benign
0.65

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: rs1061122; hg19: chr1-154832290; COSMIC: COSV55215271; API