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rs1799884

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.555

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
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
GCKNM_000162.5 linkuse as main transcript upstream_gene_variant ENST00000403799.8
GCKNM_001354800.1 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GCKENST00000403799.8 linkuse as main transcript upstream_gene_variant 1 NM_000162.5 P1P35557-1

Frequencies

GnomAD3 genomes
AF:
0.170
AC:
25879
AN:
152068
Hom.:
2200
Cov.:
33
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 submitterclinical testingGeneDxJun 28, 2018This 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
15
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.

Other links and lift over

dbSNP: rs1799884; hg19: chr7-44229068;