GeneBe

11-128891435-C-CAGAAAGAG

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000890.5(KCNJ5):​c.-296_-295insGAAAGAGA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 84,712 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000012 ( 0 hom., cov: 26)

Consequence

KCNJ5
NM_000890.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.342

Publications

0 publications found
Variant links:
Genes affected
KCNJ5 (HGNC:6266): (potassium inwardly rectifying channel subfamily J member 5) This gene encodes an integral membrane protein which belongs to one of seven subfamilies of inward-rectifier potassium channel proteins called potassium channel subfamily J. The encoded protein is a subunit of the potassium channel which is homotetrameric. It is controlled by G-proteins and has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Naturally occurring mutations in this gene are associated with aldosterone-producing adenomas. [provided by RefSeq, Aug 2017]
KCNJ5-AS1 (HGNC:28584): (KCNJ5 antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNJ5NM_000890.5 linkc.-296_-295insGAAAGAGA 5_prime_UTR_variant Exon 1 of 3 ENST00000529694.6 NP_000881.3 P48544A0A5J6E2W8
KCNJ5NM_001354169.2 linkc.-385_-384insGAAAGAGA 5_prime_UTR_variant Exon 1 of 4 NP_001341098.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNJ5ENST00000529694.6 linkc.-296_-295insGAAAGAGA 5_prime_UTR_variant Exon 1 of 3 1 NM_000890.5 ENSP00000433295.1 P48544
KCNJ5-AS1ENST00000730925.1 linkn.314+12995_314+12996insCTCTTTCT intron_variant Intron 2 of 2
KCNJ5-AS1ENST00000730926.1 linkn.285+12995_285+12996insCTCTTTCT intron_variant Intron 2 of 2
KCNJ5ENST00000338350.4 linkc.-386_-385insAGAAAGAG upstream_gene_variant 1 ENSP00000339960.4 P48544

Frequencies

GnomAD3 genomes
AF:
0.0000118
AC:
1
AN:
84712
Hom.:
0
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.0000519
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.0000118
AC:
1
AN:
84712
Hom.:
0
Cov.:
26
AF XY:
0.00
AC XY:
0
AN XY:
39972
show subpopulations
African (AFR)
AF:
0.0000519
AC:
1
AN:
19286
American (AMR)
AF:
0.00
AC:
0
AN:
8906
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2140
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2410
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1986
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
5008
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
162
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
43298
Other (OTH)
AF:
0.00
AC:
0
AN:
1060
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.925
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs886047994; hg19: chr11-128761330; API