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GeneBe

rs780094

Variant summary

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

The NM_001486.4(GCKR):c.1423-418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,110 control chromosomes in the GnomAD database, including 34,550 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 0.66 ( 34550 hom., cov: 32)

Consequence

GCKR
NM_001486.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185
Variant links:
Genes affected
GCKR (HGNC:4196): (glucokinase regulator) This gene encodes a protein belonging to the GCKR subfamily of the SIS (Sugar ISomerase) family of proteins. The gene product is a regulatory protein that inhibits glucokinase in liver and pancreatic islet cells by binding non-covalently to form an inactive complex with the enzyme. This gene is considered a susceptibility gene candidate for a form of maturity-onset diabetes of the young (MODY). [provided by RefSeq, Jul 2008]

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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 = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GCKRNM_001486.4 linkuse as main transcriptc.1423-418T>C intron_variant ENST00000264717.7
GCKRXM_017003796.2 linkuse as main transcriptc.853-418T>C intron_variant
GCKRXM_017003797.2 linkuse as main transcriptc.853-418T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GCKRENST00000264717.7 linkuse as main transcriptc.1423-418T>C intron_variant 1 NM_001486.4 P1

Frequencies

GnomAD3 genomes
AF:
0.664
AC:
100893
AN:
151992
Hom.:
34482
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.825
Gnomad AMI
AF:
0.705
Gnomad AMR
AF:
0.618
Gnomad ASJ
AF:
0.456
Gnomad EAS
AF:
0.512
Gnomad SAS
AF:
0.762
Gnomad FIN
AF:
0.632
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.598
Gnomad OTH
AF:
0.597
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.664
AC:
101032
AN:
152110
Hom.:
34550
Cov.:
32
AF XY:
0.663
AC XY:
49313
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.825
Gnomad4 AMR
AF:
0.618
Gnomad4 ASJ
AF:
0.456
Gnomad4 EAS
AF:
0.512
Gnomad4 SAS
AF:
0.763
Gnomad4 FIN
AF:
0.632
Gnomad4 NFE
AF:
0.598
Gnomad4 OTH
AF:
0.601
Alfa
AF:
0.595
Hom.:
63307
Bravo
AF:
0.667
Asia WGS
AF:
0.692
AC:
2404
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
2.6
Dann
Benign
0.59

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

LitVar

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

Other links and lift over

dbSNP: rs780094; hg19: chr2-27741237; API