rs9826659
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001146156.2(GSK3B):c.1196-5409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,200 control chromosomes in the GnomAD database, including 5,073 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 0.23 ( 5073 hom., cov: 32)
Consequence
GSK3B
NM_001146156.2 intron
NM_001146156.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.586
Genes affected
GSK3B (HGNC:4617): (glycogen synthase kinase 3 beta) The protein encoded by this gene is a serine-threonine kinase belonging to the glycogen synthase kinase subfamily. It is a negative regulator of glucose homeostasis and is involved in energy metabolism, inflammation, ER-stress, mitochondrial dysfunction, and apoptotic pathways. Defects in this gene have been associated with Parkinson disease and Alzheimer disease. [provided by RefSeq, Aug 2017]
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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
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSK3B | NM_001146156.2 | c.1196-5409T>C | intron_variant | ENST00000264235.13 | |||
GSK3B | NM_001354596.2 | c.1097-5409T>C | intron_variant | ||||
GSK3B | NM_002093.4 | c.1235-5409T>C | intron_variant | ||||
GSK3B | XM_006713610.4 | c.1136-5409T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSK3B | ENST00000264235.13 | c.1196-5409T>C | intron_variant | 1 | NM_001146156.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.231 AC: 35188AN: 152082Hom.: 5073 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.231 AC: 35178AN: 152200Hom.: 5073 Cov.: 32 AF XY: 0.230 AC XY: 17098AN XY: 74394
GnomAD4 genome
?
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32
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17098
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74394
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555
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at