rs2836252

chr21-38261465-A-Cchr21-38261465-A-T

Variant summary

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

The NM_170736.3(KCNJ15):c.-117+4280A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,158 control chromosomes in the GnomAD database, including 3,224 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 0.20 (3224 hom., cov: 32)
• Consequence: KCNJ15 NM_170736.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

KCNJ15 (HGNC:6261): (potassium inwardly rectifying channel subfamily J member 15) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Eight transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ15	NM_170736.3	c.-117+4280A>C		intron_variant		ENST00000398938.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ15	ENST00000398938.7	c.-117+4280A>C		intron_variant		1	NM_170736.3	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30226 AN: 152040 Hom.: 3209 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.199 AC: 30281 AN: 152158 Hom.: 3224 Cov.: 32 AF XY: 0.201 AC XY: 14950 AN XY: 74396

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.167

Alfa AF: 0.193 Hom.: 361

Bravo AF: 0.197

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.4
Dann	Benign	0.86

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: rs2836252; hg19: chr21-39633387;