rs6676862

Variant names:

• chr1-159999218-C-T
• rs6676862
• ENST00000639408:c.*240G>A

Variant summary

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

The ENST00000639408(KCNJ10):​c.*240G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 384,180 control chromosomes in the GnomAD database, including 8,637 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 0.22 (4009 hom., cov: 31)
  • Exomes 𝑓: 0.19 (4628 hom.)
• Consequence: KCNJ10 ENST00000639408 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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]

LOC124904436 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904436	XR_007066682.1	n.1548G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ10	ENST00000639408	c.*240G>A		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000491635.1
KCNJ10	ENST00000637644	c.*251G>A		3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000490282.1
KCNJ10	ENST00000640914.1	c.*308G>A		3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000491175.1
KCNJ10	ENST00000509700.2	c.*202G>A		downstream_gene_variant		5		ENSP00000491416.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33532 AN: 151844 Hom.: 4010 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.192 AC: 44676 AN: 232218 Hom.: 4628 Cov.: 0 AF XY: 0.191 AC XY: 22549 AN XY: 117886

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.292

Gnomad4 ASJ exome AF: 0.286

Gnomad4 EAS exome AF: 0.0497

Gnomad4 SAS exome AF: 0.130

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.201

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.221 AC: 33548 AN: 151962 Hom.: 4009 Cov.: 31 AF XY: 0.222 AC XY: 16476 AN XY: 74312

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.206

Alfa AF: 0.212 Hom.: 4780

Bravo AF: 0.234

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6676862; hg19: chr1-159969008;