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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(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 151992 control chromosomes in the gnomAD Genomes database, including 34482 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 ( 34482 hom., cov: 32)

Consequence

GCKR
NM_001486 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

Links

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
?
GnomAd 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
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
3.7
Dann
Benign
0.59

Splicing

Find out SpliceAI 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;