1-154718969-C-T

Position:

• chr1-154718969-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.1702-3966G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,066 control chromosomes in the GnomAD database, including 30,829 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 0.63 (30829 hom., cov: 32)
• Consequence: KCNN3 NM_002249.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.751

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNN3	NM_002249.6	c.1702-3966G>A		intron_variant		ENST00000271915.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNN3	ENST00000271915.9	c.1702-3966G>A		intron_variant		1	NM_002249.6	P1
KCNN3	ENST00000358505.2	c.763-3966G>A		intron_variant		1
KCNN3	ENST00000361147.8	c.787-3966G>A		intron_variant		1
KCNN3	ENST00000618040.4	c.1747-3966G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95432 AN: 151946 Hom.: 30821 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.628 AC: 95460 AN: 152066 Hom.: 30829 Cov.: 32 AF XY: 0.633 AC XY: 47052 AN XY: 74358

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.627

Alfa AF: 0.671 Hom.: 69332

Bravo AF: 0.619

Asia WGS AF: 0.699 AC: 2432 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	2.9
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs10128027; hg19: chr1-154691445;