rs775617188
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000158.4(GBE1):c.2103G>A(p.Pro701Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,612,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
GBE1
NM_000158.4 synonymous
NM_000158.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.515
Genes affected
GBE1 (HGNC:4180): (1,4-alpha-glucan branching enzyme 1) The protein encoded by this gene is a glycogen branching enzyme that catalyzes the transfer of alpha-1,4-linked glucosyl units from the outer end of a glycogen chain to an alpha-1,6 position on the same or a neighboring glycogen chain. Branching of the chains is essential to increase the solubility of the glycogen molecule and, consequently, in reducing the osmotic pressure within cells. Highest level of this enzyme are found in liver and muscle. Mutations in this gene are associated with glycogen storage disease IV (also known as Andersen's disease). [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 3-81490413-C-T is Benign according to our data. Variant chr3-81490413-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 764278.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.515 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBE1 | ENST00000429644.7 | c.2103G>A | p.Pro701Pro | synonymous_variant | Exon 16 of 16 | 1 | NM_000158.4 | ENSP00000410833.2 | ||
GBE1 | ENST00000489715.1 | c.1980G>A | p.Pro660Pro | synonymous_variant | Exon 16 of 16 | 2 | ENSP00000419638.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
2
AN:
151988
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:
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248702Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134970
GnomAD3 exomes
AF:
AC:
6
AN:
248702
Hom.:
AF XY:
AC XY:
3
AN XY:
134970
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460642Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726672
GnomAD4 exome
AF:
AC:
13
AN:
1460642
Hom.:
Cov.:
29
AF XY:
AC XY:
6
AN XY:
726672
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74198
GnomAD4 genome
AF:
AC:
2
AN:
151988
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74198
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disease, type IV Benign:1
Dec 02, 2020
Natera, Inc.
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Glycogen storage disease, type IV;C1856301:Glycogen storage disease IV, classic hepatic Benign:1
Jan 13, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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