rs1557765

Variant summary

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

The ENST00000568280.1(ENSG00000260196):​n.1444T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,212 control chromosomes in the GnomAD database, including 38,474 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 0.70 ( 38459 hom., cov: 33)
Exomes 𝑓: 0.65 ( 15 hom. )

Consequence


ENST00000568280.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28
Variant links:
Genes affected
KCNJ11 (HGNC:6257): (potassium inwardly rectifying channel subfamily J member 11) 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, which has a greater tendency to allow potassium to flow into a cell rather than out of a cell, is controlled by G-proteins and is found associated with the sulfonylurea receptor SUR. Mutations in this gene are a cause of familial persistent hyperinsulinemic hypoglycemia of infancy (PHHI), an autosomal recessive disorder characterized by unregulated insulin secretion. Defects in this gene may also contribute to autosomal dominant non-insulin-dependent diabetes mellitus type II (NIDDM), transient neonatal diabetes mellitus type 3 (TNDM3), and permanent neonatal diabetes mellitus (PNDM). Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Oct 2009]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000568280.1 linkuse as main transcriptn.1444T>C non_coding_transcript_exon_variant 1/1
KCNJ11ENST00000682764.1 linkuse as main transcriptc.*50+4777A>G intron_variant ENSP00000506780 Q14654-2

Frequencies

GnomAD3 genomes
AF:
0.698
AC:
106151
AN:
152028
Hom.:
38411
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.907
Gnomad AMI
AF:
0.505
Gnomad AMR
AF:
0.666
Gnomad ASJ
AF:
0.641
Gnomad EAS
AF:
0.646
Gnomad SAS
AF:
0.625
Gnomad FIN
AF:
0.519
Gnomad MID
AF:
0.718
Gnomad NFE
AF:
0.621
Gnomad OTH
AF:
0.684
GnomAD4 exome
AF:
0.652
AC:
43
AN:
66
Hom.:
15
Cov.:
0
AF XY:
0.620
AC XY:
31
AN XY:
50
show subpopulations
Gnomad4 EAS exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.679
Gnomad4 OTH exome
AF:
0.333
GnomAD4 genome
AF:
0.698
AC:
106260
AN:
152146
Hom.:
38459
Cov.:
33
AF XY:
0.693
AC XY:
51562
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.907
Gnomad4 AMR
AF:
0.666
Gnomad4 ASJ
AF:
0.641
Gnomad4 EAS
AF:
0.647
Gnomad4 SAS
AF:
0.625
Gnomad4 FIN
AF:
0.519
Gnomad4 NFE
AF:
0.621
Gnomad4 OTH
AF:
0.683
Alfa
AF:
0.645
Hom.:
18616
Bravo
AF:
0.714
Asia WGS
AF:
0.665
AC:
2314
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.59
DANN
Benign
0.56

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.

Other links and lift over

dbSNP: rs1557765; hg19: chr11-17403639; API