chr21-37911752-G-T

Position:

• chr21-37911752-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_002240.5(KCNJ6):​c.-28+4132C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 152,202 control chromosomes in the GnomAD database, including 26 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 0.015 (26 hom., cov: 33)
• Consequence: KCNJ6 NM_002240.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (2243/152202) while in subpopulation NFE AF= 0.023 (1562/67984). AF 95% confidence interval is 0.022. There are 26 homozygotes in gnomad4. There are 1114 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2243 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KCNJ6	NM_002240.5	c.-28+4132C>A		intron_variant		ENST00000609713.2	NP_002231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KCNJ6	ENST00000609713.2	c.-28+4132C>A		intron_variant		1	NM_002240.5	ENSP00000477437.1
KCNJ6	ENST00000645093.1	c.-27-71043C>A		intron_variant				ENSP00000493772.1

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2242 AN: 152084 Hom.: 26 Cov.: 33

Gnomad AFR AF: 0.00403

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00655

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00291

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0147 AC: 2243 AN: 152202 Hom.: 26 Cov.: 33 AF XY: 0.0150 AC XY: 1114 AN XY: 74406

Gnomad4 AFR AF: 0.00402

Gnomad4 AMR AF: 0.00660

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00291

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0230

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0182 Hom.: 3

Bravo AF: 0.0127

Asia WGS AF: 0.00202 AC: 7 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2226360; hg19: chr21-39284055;