21-37833852-A-C

Variant summary

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

The NM_002240.5(KCNJ6):c.25+6806T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,148 control chromosomes in the GnomAD database, including 43,305 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 0.75 (43305 hom., cov: 32)
• Consequence: KCNJ6 NM_002240.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670

Genes affected

KCNJ6 (HGNC:6267): (potassium inwardly rectifying channel subfamily J member 6) This gene encodes a member of the G protein-coupled inwardly-rectifying potassium channel family of inward rectifier potassium channels. This type of potassium channel allows a greater flow of potassium into the cell than out of it. These proteins modulate many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells, through G-protein coupled receptor stimulation. Mutations in this gene are associated with Keppen-Lubinsky Syndrome, a rare condition characterized by severe developmental delay, facial dysmorphism, and intellectual disability. [provided by RefSeq, Apr 2015]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ6	NM_002240.5	c.25+6806T>G		intron_variant		ENST00000609713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ6	ENST00000609713.2	c.25+6806T>G		intron_variant		1	NM_002240.5	P1
	ENST00000692486.2	n.177-6576A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113387 AN: 152030 Hom.: 43250 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.746 AC: 113501 AN: 152148 Hom.: 43305 Cov.: 32 AF XY: 0.749 AC XY: 55704 AN XY: 74350

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.749

Alfa AF: 0.672 Hom.: 14884

Bravo AF: 0.760

Asia WGS AF: 0.921 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	7.3
Dann	Benign	0.51

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: rs991985; hg19: chr21-39206154;