21-38256530-C-G

Variant summary

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

The NM_001276437.2(KCNJ15):c.-198-574C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 151,174 control chromosomes in the GnomAD database, including 2,126 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 0.15 (2126 hom., cov: 29)
• Consequence: KCNJ15 NM_001276437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ15	NM_001276437.2	c.-198-574C>G		intron_variant
KCNJ15	NM_001276438.2	c.-117+26507C>G		intron_variant
KCNJ15	NM_001276439.2	c.-256-516C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ15	ENST00000547341.5	c.-398-516C>G		intron_variant		3
KCNJ15	ENST00000547595.5	c.-116-40396C>G		intron_variant		2
KCNJ15	ENST00000548700.5	c.-107-40396C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22064 AN: 151058 Hom.: 2119 Cov.: 29

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.146 AC: 22081 AN: 151174 Hom.: 2126 Cov.: 29 AF XY: 0.153 AC XY: 11300 AN XY: 73858

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0886 Hom.: 130

Bravo AF: 0.137

Asia WGS AF: 0.336 AC: 1170 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.86
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13433471; hg19: chr21-39628452;