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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

Links

GCKR (HGNC:4196):

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	Effect	MANE
GCKR	NM_001486.4 linkuse as main transcript	c.1423-418T>C	intron_variant	ENST00000264717.7
GCKR	XM_017003796.2 linkuse as main transcript	c.853-418T>C	intron_variant
GCKR	XM_017003797.2 linkuse as main transcript	c.853-418T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCKR	ENST00000264717.7 linkuse as main transcript	c.1423-418T>C		intron_variant		1	NM_001486.4	P1

Frequencies

GnomAD3 genomes

AF:

0.664

AC:

100893

AN:

151992

Hom.:

34482

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over