rs1053074

chr1-160039331-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_002241.5(KCNJ10):c.*2062T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,462 control chromosomes in the GnomAD database, including 16,696 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (16616 hom., cov: 28)
  • Exomes 𝑓: 0.36 (80 hom.)
• Consequence: KCNJ10 NM_002241.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.67

Genes affected

KCNJ10 (HGNC:6256): (potassium inwardly rectifying channel subfamily J member 10) This gene encodes a member of the inward rectifier-type potassium channel family, characterized by having a greater tendency to allow potassium to flow into, rather than out of, a cell. The encoded protein may form a heterodimer with another potassium channel protein and may be responsible for the potassium buffering action of glial cells in the brain. Mutations in this gene have been associated with seizure susceptibility of common idiopathic generalized epilepsy syndromes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP6: Variant 1-160039331-A-C is Benign according to our data. Variant chr1-160039331-A-C is described in ClinVar as [Benign]. Clinvar id is 293090.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ10	NM_002241.5	c.*2062T>G		3_prime_UTR_variant	2/2	ENST00000644903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ10	ENST00000644903.1	c.*2062T>G		3_prime_UTR_variant	2/2		NM_002241.5	P1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 68675 AN: 150496 Hom.: 16600 Cov.: 28

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.419

GnomAD4 exome AF: 0.365 AC: 310 AN: 850 Hom.: 80 Cov.: 0 AF XY: 0.355 AC XY: 210 AN XY: 592

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.358

Gnomad4 NFE exome AF: 0.367

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.456 AC: 68736 AN: 150612 Hom.: 16616 Cov.: 28 AF XY: 0.452 AC XY: 33245 AN XY: 73510

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.418

Alfa AF: 0.410 Hom.: 17611

Bravo AF: 0.467

Asia WGS AF: 0.394 AC: 1363 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

- -

Autosomal recessive nonsyndromic hearing loss 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

EAST syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	5.8
Dann	Benign	0.68

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: rs1053074; hg19: chr1-160009121; COSMIC: COSV63635370;