rs1787422

chr21-37704659-C-T

Variant summary

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

The NM_002240.5(KCNJ6):c.946+9552G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 148,612 control chromosomes in the GnomAD database, including 498 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 0.048 (498 hom., cov: 30)
• Consequence: KCNJ6 NM_002240.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

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]

KCNJ6-AS1 (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 (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ6	NM_002240.5	c.946+9552G>A		intron_variant		ENST00000609713.2
KCNJ6-AS1	NR_183540.1	n.548-5655C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ6	ENST00000609713.2	c.946+9552G>A		intron_variant		1	NM_002240.5	P1
KCNJ6-AS1	ENST00000711629.1	n.141-5655C>T		intron_variant, non_coding_transcript_variant
KCNJ6	ENST00000645093.1	c.946+9552G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.0474 AC: 7046 AN: 148498 Hom.: 497 Cov.: 30

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.000905

Gnomad EAS AF: 0.000198

Gnomad SAS AF: 0.0158

Gnomad FIN AF: 0.000382

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0476 AC: 7071 AN: 148612 Hom.: 498 Cov.: 30 AF XY: 0.0464 AC XY: 3373 AN XY: 72740

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.000905

Gnomad4 EAS AF: 0.000198

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.000382

Gnomad4 NFE AF: 0.00379

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.544 Hom.: 18586

Asia WGS AF: 0.0240 AC: 82 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.54

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: rs1787422; hg19: chr21-39076961; COSMIC: COSV55708914;