19-42232623-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000222330.8(GSK3A):​c.1158C>T​(p.Tyr386=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000347 in 1,613,154 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 1 hom. )

Consequence

GSK3A
ENST00000222330.8 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.62
Variant links:
Genes affected
GSK3A (HGNC:4616): (glycogen synthase kinase 3 alpha) This gene encodes a multifunctional Ser/Thr protein kinase that is implicated in the control of several regulatory proteins including glycogen synthase, and transcription factors, such as JUN. It also plays a role in the WNT and PI3K signaling pathways, as well as regulates the production of beta-amyloid peptides associated with Alzheimer's disease. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 19-42232623-G-A is Benign according to our data. Variant chr19-42232623-G-A is described in ClinVar as [Benign]. Clinvar id is 720784.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 296 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GSK3ANM_019884.3 linkuse as main transcriptc.1158C>T p.Tyr386= synonymous_variant 9/11 ENST00000222330.8 NP_063937.2
GSK3AXR_001753673.2 linkuse as main transcriptn.1295C>T non_coding_transcript_exon_variant 9/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GSK3AENST00000222330.8 linkuse as main transcriptc.1158C>T p.Tyr386= synonymous_variant 9/111 NM_019884.3 ENSP00000222330 P2

Frequencies

GnomAD3 genomes
AF:
0.00194
AC:
295
AN:
152138
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00686
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.000512
AC:
128
AN:
249992
Hom.:
0
AF XY:
0.000318
AC XY:
43
AN XY:
135038
show subpopulations
Gnomad AFR exome
AF:
0.00751
Gnomad AMR exome
AF:
0.0000871
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000886
Gnomad OTH exome
AF:
0.000329
GnomAD4 exome
AF:
0.000180
AC:
263
AN:
1460898
Hom.:
1
Cov.:
31
AF XY:
0.000158
AC XY:
115
AN XY:
726724
show subpopulations
Gnomad4 AFR exome
AF:
0.00681
Gnomad4 AMR exome
AF:
0.000202
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000540
Gnomad4 OTH exome
AF:
0.000331
GnomAD4 genome
AF:
0.00194
AC:
296
AN:
152256
Hom.:
1
Cov.:
32
AF XY:
0.00171
AC XY:
127
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.00686
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.000999
Hom.:
1
Bravo
AF:
0.00226

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 testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
8.3
DANN
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs146606692; hg19: chr19-42736775; API