Genetic Variant KCNJ15:p.Met30Val (chr21-38299349-A-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_170736.3(KCNJ15):c.88A>G(p.Met30Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

KCNJ15
NM_170736.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.00

Publications

0 publications found

Variant links:

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]

KCNJ15 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.14184317).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNJ15	NM_170736.3 link	c.88A>G	p.Met30Val	missense_variant	Exon 3 of 3	ENST00000398938.7	NP_733932.1	Q99712

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNJ15	ENST00000398938.7 link	c.88A>G	p.Met30Val	missense_variant	Exon 3 of 3	1	NM_170736.3	ENSP00000381911.2		Q99712

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1461876

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727240

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00000180

AC:

AN:

1111996

Other (OTH)

AF:

0.00

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Uncertain

0.028

BayesDel_noAF

Benign

-0.20

CADD

Benign

(source)

DANN

Benign

0.45

DEOGEN2

Benign

0.026

.;.;.;.;.;.;T;T;.;T;T;T;T;T;.;T;T;T;T

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.16

FATHMM_MKL

Uncertain

0.82

LIST_S2

Uncertain

0.88

.;.;.;.;.;D;.;T;T;.;.;D;.;.;T;.;.;T;T

M_CAP

Benign

0.027

MetaRNN

Benign

0.14

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.36

MutationAssessor

Benign

-0.99

.;.;.;.;.;.;N;N;.;.;N;.;N;N;.;N;N;.;.

PhyloP100

5.0

PrimateAI

Uncertain

0.58

PROVEAN

Benign

-1.0

N;N;N;N;N;N;.;.;N;N;N;N;N;N;N;N;N;N;N

REVEL

Uncertain

0.40

Sift

Uncertain

0.015

D;D;D;D;D;D;.;.;T;T;T;D;T;T;T;T;T;T;T

Sift4G

Benign

0.063

T;T;T;T;T;T;T;T;T;T;T;D;T;T;T;T;T;T;T

Polyphen

0.0050

.;.;.;.;.;.;B;B;.;.;B;.;B;B;.;B;B;.;.

Vest4

0.15, 0.12, 0.098, 0.099, 0.10

MutPred

0.37

Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);Loss of catalytic residue at M30 (P = 0.057);

MVP

0.78

MPC

0.45

ClinPred

0.56

GERP RS

5.1

Varity_R

0.26

gMVP

0.56

Mutation Taster

=90/10

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over