1-154869723-GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT-GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT

Position:

• chr1-154869723-GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT-GGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_002249.6(KCNN3):​c.241_242insAGCAGCAGCAGC​(p.Gln77_Gln80dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.22 (3689 hom., cov: 0)
  • Exomes 𝑓: 0.24 (7801 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNN3 NM_002249.6 inframe_insertion
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 2.12

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 -16 ACMG points.

• BP6: Variant 1-154869723-G-GGCTGCTGCTGCT is Benign according to our data. Variant chr1-154869723-G-GGCTGCTGCTGCT is described in ClinVar as [Benign]. Clinvar id is 403003.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNN3	NM_002249.6	c.241_242insAGCAGCAGCAGC	p.Gln77_Gln80dup	inframe_insertion	1/8	ENST00000271915.9
KCNN3	NM_001204087.2	c.241_242insAGCAGCAGCAGC	p.Gln77_Gln80dup	inframe_insertion	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNN3	ENST00000271915.9	c.241_242insAGCAGCAGCAGC	p.Gln77_Gln80dup	inframe_insertion	1/8	1	NM_002249.6	P1
KCNN3	ENST00000618040.4	c.241_242insAGCAGCAGCAGC	p.Gln77_Gln80dup	inframe_insertion	1/9	5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 31115 AN: 140772 Hom.: 3688 Cov.: 0

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.0733

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.236 AC: 302058 AN: 1280232 Hom.: 7801 Cov.: 112 AF XY: 0.235 AC XY: 148196 AN XY: 631724

Gnomad4 AFR exome AF: 0.207

Gnomad4 AMR exome AF: 0.216

Gnomad4 ASJ exome AF: 0.190

Gnomad4 EAS exome AF: 0.249

Gnomad4 SAS exome AF: 0.189

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.221 AC: 31142 AN: 140870 Hom.: 3689 Cov.: 0 AF XY: 0.222 AC XY: 15036 AN XY: 67734

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.189

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 25, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3831942; hg19: chr1-154842199;