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
ENST00000476008.1 intron, non_coding_transcript
Scores
2
Clinical Significance
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 |
---|---|---|---|---|---|---|---|
GCK | NM_000162.5 | upstream_gene_variant | ENST00000403799.8 | ||||
GCK | NM_001354800.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCK | ENST00000403799.8 | upstream_gene_variant | 1 | NM_000162.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.170 AC: 25879AN: 152068Hom.: 2200 Cov.: 33
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GnomAD4 exome AF: 0.141 AC: 6757AN: 47754Hom.: 579 AF XY: 0.141 AC XY: 3486AN XY: 24720
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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
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at