chr1-154719612-T-C

Position:

• chr1-154719612-T-C

Variant summary

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

The NM_002249.6(KCNN3):​c.1702-4609A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,982 control chromosomes in the GnomAD database, including 22,986 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 0.52 (22986 hom., cov: 31)
• Consequence: KCNN3 NM_002249.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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 (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNN3	NM_002249.6	c.1702-4609A>G		intron_variant		ENST00000271915.9	NP_002240.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNN3	ENST00000271915.9	c.1702-4609A>G		intron_variant		1	NM_002249.6	ENSP00000271915	P1
KCNN3	ENST00000358505.2	c.763-4609A>G		intron_variant		1		ENSP00000351295
KCNN3	ENST00000361147.8	c.787-4609A>G		intron_variant		1		ENSP00000354764
KCNN3	ENST00000618040.4	c.1747-4609A>G		intron_variant		5		ENSP00000481848

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78313 AN: 151864 Hom.: 22941 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.516 AC: 78417 AN: 151982 Hom.: 22986 Cov.: 31 AF XY: 0.508 AC XY: 37765 AN XY: 74272

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.460

Alfa AF: 0.430 Hom.: 20348

Bravo AF: 0.530

Asia WGS AF: 0.412 AC: 1437 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	0.29
DANN	Benign	0.59

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: rs4845663; hg19: chr1-154692088;