rs883319

chr1-154785946-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002249.6(KCNN3):c.1030-13553G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,018 control chromosomes in the GnomAD database, including 3,157 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 0.20 (3157 hom., cov: 32)
• Consequence: KCNN3 NM_002249.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNN3	NM_002249.6	c.1030-13553G>A		intron_variant		ENST00000271915.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNN3	ENST00000271915.9	c.1030-13553G>A		intron_variant		1	NM_002249.6	P1
KCNN3	ENST00000358505.2	c.91-13553G>A		intron_variant		1
KCNN3	ENST00000361147.8	c.115-13553G>A		intron_variant		1
KCNN3	ENST00000618040.4	c.1030-13553G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30557 AN: 151902 Hom.: 3153 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30562 AN: 152018 Hom.: 3157 Cov.: 32 AF XY: 0.201 AC XY: 14938 AN XY: 74302

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.201

Alfa AF: 0.216 Hom.: 7316

Bravo AF: 0.201

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.36

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

Other links and lift over

dbSNP: rs883319; hg19: chr1-154758422;