rs10752609

Variant names:

• chr1-154818652-G-A
• rs10752609
• NM_002249.6:c.1029+3437C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-154818652-G-A
• chr1-154818652-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002249.6(KCNN3):​c.1029+3437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,082 control chromosomes in the GnomAD database, including 27,535 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 0.58 (27535 hom., cov: 32)
• Consequence: KCNN3 NM_002249.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 6 publications found

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]

KCNN3 Gene-Disease associations (from GenCC):

• Zimmermann-Laband syndrome 3

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• Zimmermann-Laband syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• schizophrenia

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002249.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNN3	NM_002249.6	MANE Select	c.1029+3437C>T		intron	N/A	NP_002240.3
	KCNN3	NM_001204087.2		c.1029+3437C>T		intron	N/A	NP_001191016.1
	KCNN3	NM_001365837.1		c.90+3437C>T		intron	N/A	NP_001352766.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNN3	ENST00000271915.9	TSL:1 MANE Select	c.1029+3437C>T		intron	N/A	ENSP00000271915.3
	KCNN3	ENST00000361147.8	TSL:1	c.114+3437C>T		intron	N/A	ENSP00000354764.4
	KCNN3	ENST00000358505.2	TSL:1	c.90+3437C>T		intron	N/A	ENSP00000351295.2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88536 AN: 151964 Hom.: 27493 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.583 AC: 88640 AN: 152082 Hom.: 27535 Cov.: 32 AF XY: 0.581 AC XY: 43183 AN XY: 74346

African (AFR) AF: 0.784 AC: 32519 AN: 41500

American (AMR) AF: 0.630 AC: 9627 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1503 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4218 AN: 5170

South Asian (SAS) AF: 0.434 AC: 2091 AN: 4822

European-Finnish (FIN) AF: 0.484 AC: 5106 AN: 10558

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32084 AN: 67970

Other (OTH) AF: 0.527 AC: 1110 AN: 2106

Alfa AF: 0.495 Hom.: 36693

Bravo AF: 0.608

Asia WGS AF: 0.650 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		0.18
Mutation Taster		=16/84	disease causing

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

Other links and lift over

dbSNP: rs10752609; hg19: chr1-154791128;