21-38045687-G-A

Variant names:

• chr21-38045687-G-A
• rs12482611
• ENST00000645093.1:c.-28+74620C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645093.1(KCNJ6):​c.-28+74620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,174 control chromosomes in the GnomAD database, including 1,254 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 0.099 (1254 hom., cov: 33)
• Consequence: KCNJ6 ENST00000645093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88
• Publications: 1 publications found

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]

DSCR4 (HGNC:3045): (Down syndrome critical region 4) The gene is found in a region of chromosome 21 that has been linked to the pathogenesis of Down syndrome. This gene is transcribed from a bi-directional promoter located in an endogenous retrovirus. [provided by RefSeq, Jan 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645093.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCNJ6	ENST00000645093.1		c.-28+74620C>T		intron	N/A	ENSP00000493772.1
	DSCR4	ENST00000398948.5	TSL:5	n.314+74620C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0990 AC: 15057 AN: 152056 Hom.: 1247 Cov.: 33

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0800

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0991 AC: 15075 AN: 152174 Hom.: 1254 Cov.: 33 AF XY: 0.108 AC XY: 8049 AN XY: 74408

African (AFR) AF: 0.0377 AC: 1567 AN: 41546

American (AMR) AF: 0.147 AC: 2252 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5170

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10570

Middle Eastern (MID) AF: 0.121 AC: 35 AN: 290

European-Non Finnish (NFE) AF: 0.0801 AC: 5443 AN: 67992

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.0915 Hom.: 1376

Bravo AF: 0.0960

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.24
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12482611; hg19: chr21-39417989;