rs17204365
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_001146156.2(GSK3B):c.367-8819A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0244 in 152,312 control chromosomes in the GnomAD database, including 64 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 0.024 ( 64 hom., cov: 32)
Consequence
GSK3B
NM_001146156.2 intron
NM_001146156.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.896
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0244 (3714/152312) while in subpopulation AMR AF= 0.0369 (565/15302). AF 95% confidence interval is 0.0344. There are 64 homozygotes in gnomad4. There are 1865 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 3714 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GSK3B | NM_001146156.2 | c.367-8819A>G | intron_variant | ENST00000264235.13 | |||
GSK3B | NM_001354596.2 | c.367-8819A>G | intron_variant | ||||
GSK3B | NM_002093.4 | c.367-8819A>G | intron_variant | ||||
GSK3B | XM_006713610.4 | c.367-8819A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSK3B | ENST00000264235.13 | c.367-8819A>G | intron_variant | 1 | NM_001146156.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0244 AC: 3712AN: 152194Hom.: 64 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: 0.0244 AC: 3714AN: 152312Hom.: 64 Cov.: 32 AF XY: 0.0250 AC XY: 1865AN XY: 74476
GnomAD4 genome
?
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3714
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152312
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32
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1865
AN XY:
74476
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12
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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