chr21-38234847-C-T

Variant names:

• chr21-38234847-C-T
• rs2186344
• NM_001276437.2:c.-199+4824C>T

Variant summary

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

The NM_001276437.2(KCNJ15):​c.-199+4824C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,000 control chromosomes in the GnomAD database, including 17,005 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 0.46 (17005 hom., cov: 33)
• Consequence: KCNJ15 NM_001276437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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]

ENSG00000289927 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNJ15	NM_001276437.2	c.-199+4824C>T		intron_variant	Intron 1 of 3		NP_001263366.1
KCNJ15	NM_001276438.2	c.-117+4824C>T		intron_variant	Intron 1 of 2		NP_001263367.1
KCNJ15	NM_001276439.2	c.-257+4824C>T		intron_variant	Intron 1 of 3		NP_001263368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ15	ENST00000547341.5	c.-398-22199C>T		intron_variant	Intron 1 of 4	3		ENSP00000447111.1
KCNJ15	ENST00000547595.5	c.-116-62079C>T		intron_variant	Intron 1 of 2	2		ENSP00000450254.1
KCNJ15	ENST00000548700.5	c.-107-62079C>T		intron_variant	Intron 1 of 2	3		ENSP00000448886.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70123 AN: 151882 Hom.: 16976 Cov.: 33

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.462 AC: 70185 AN: 152000 Hom.: 17005 Cov.: 33 AF XY: 0.475 AC XY: 35273 AN XY: 74290

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.499

Alfa AF: 0.424 Hom.: 7267

Bravo AF: 0.451

Asia WGS AF: 0.699 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.21
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2186344; hg19: chr21-39606769;