Variant rs2186344 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000701791.1(ENSG00000289927):n.99-416C>T variant causes a intron, non coding transcript 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

ENST00000701791.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Variant links:

Genes affected

(HGNC:):

links:

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]

KCNJ15 links:

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ACMG classification

Classification made for transcript

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	Effect
KCNJ15	NM_001276437.2 linkuse as main transcript	c.-199+4824C>T	intron_variant
KCNJ15	NM_001276438.2 linkuse as main transcript	c.-117+4824C>T	intron_variant
KCNJ15	NM_001276439.2 linkuse as main transcript	c.-257+4824C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701791.1 linkuse as main transcript	n.99-416C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.462

AC:

70123

AN:

151882

Hom.:

16976

Cov.:

show subpopulations

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.:

AF XY:

0.475

AC XY:

35273

AN XY:

74290

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over