rs17204878
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001146156.2(GSK3B):c.88+35314C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,736 control chromosomes in the GnomAD database, including 24,674 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 0.53 ( 24674 hom., cov: 31)
Consequence
GSK3B
NM_001146156.2 intron
NM_001146156.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.720
Publications
5 publications found
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]
GSK3B Gene-Disease associations (from GenCC):
- neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSK3B | NM_001146156.2 | c.88+35314C>A | intron_variant | Intron 1 of 10 | ENST00000264235.13 | NP_001139628.1 | ||
GSK3B | NM_002093.4 | c.88+35314C>A | intron_variant | Intron 1 of 11 | NP_002084.2 | |||
GSK3B | NM_001354596.2 | c.88+35314C>A | intron_variant | Intron 1 of 9 | NP_001341525.1 | |||
GSK3B | XM_006713610.4 | c.88+35314C>A | intron_variant | Intron 1 of 10 | XP_006713673.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.529 AC: 80176AN: 151620Hom.: 24615 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
80176
AN:
151620
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.529 AC: 80295AN: 151736Hom.: 24674 Cov.: 31 AF XY: 0.527 AC XY: 39031AN XY: 74096 show subpopulations
GnomAD4 genome
AF:
AC:
80295
AN:
151736
Hom.:
Cov.:
31
AF XY:
AC XY:
39031
AN XY:
74096
show subpopulations
African (AFR)
AF:
AC:
35760
AN:
41468
American (AMR)
AF:
AC:
6207
AN:
15230
Ashkenazi Jewish (ASJ)
AF:
AC:
1415
AN:
3466
East Asian (EAS)
AF:
AC:
2987
AN:
5158
South Asian (SAS)
AF:
AC:
2390
AN:
4808
European-Finnish (FIN)
AF:
AC:
3931
AN:
10418
Middle Eastern (MID)
AF:
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
AC:
26095
AN:
67874
Other (OTH)
AF:
AC:
1075
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1604
3207
4811
6414
8018
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
658
1316
1974
2632
3290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1939
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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