Variant rs1799884 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The ENST00000476008.1(GCK):n.480+8222G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152068 control chromosomes in the gnomAD Genomes database, including 2200 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2200 hom., cov: 33)

Consequence

GCK
ENST00000476008.1 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.555

Links

GCK (HGNC:4195):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BP6

Variant 7-44189469-C-T is Benign according to our data. Variant chr7-44189469-C-T is described in ClinVar as [Benign]. Clinvar id is 1258742. Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GCK	NM_000162.5 linkuse as main transcript			upstream_gene_variant		ENST00000403799.8
GCK	NM_001354800.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCK	ENST00000403799.8 linkuse as main transcript			upstream_gene_variant		1	NM_000162.5	P1	P35557-1

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25879

AN:

152068

Hom.:

2200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.204

GnomAD4 exome

AF:

0.141

AC:

6757

AN:

47754

Hom.:

579

AF XY:

0.141

AC XY:

3486

AN XY:

24720

show subpopulations

Gnomad4 AFR exome

AF:

0.137

Gnomad4 AMR exome

AF:

0.201

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.153

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0905

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.149

Alfa

AF:

0.175

Hom.:

2887

Bravo

AF:

0.181

Asia WGS

AF:

0.130

AC:

455

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

This variant is associated with the following publications: (PMID: 24520939, 8603762, 19018513, 16186409, 15677518, 15173029, 21697023) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

Cadd

Benign

Dann

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over