rs7631349

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000158.4(GBE1):​c.1618+3549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,048 control chromosomes in the GnomAD database, including 6,951 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 0.30 ( 6951 hom., cov: 31)

Consequence

GBE1
NM_000158.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.120
Variant links:
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GBE1NM_000158.4 linkuse as main transcriptc.1618+3549T>C intron_variant ENST00000429644.7
GBE1XR_007095662.1 linkuse as main transcriptn.1746+3549T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GBE1ENST00000429644.7 linkuse as main transcriptc.1618+3549T>C intron_variant 1 NM_000158.4 P1
GBE1ENST00000489715.1 linkuse as main transcriptc.1495+3549T>C intron_variant 2
GBE1ENST00000484687.1 linkuse as main transcriptn.19+3549T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.297
AC:
45163
AN:
151930
Hom.:
6942
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.370
Gnomad AMI
AF:
0.237
Gnomad AMR
AF:
0.276
Gnomad ASJ
AF:
0.156
Gnomad EAS
AF:
0.438
Gnomad SAS
AF:
0.163
Gnomad FIN
AF:
0.232
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.275
Gnomad OTH
AF:
0.281
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.297
AC:
45218
AN:
152048
Hom.:
6951
Cov.:
31
AF XY:
0.293
AC XY:
21773
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.371
Gnomad4 AMR
AF:
0.276
Gnomad4 ASJ
AF:
0.156
Gnomad4 EAS
AF:
0.439
Gnomad4 SAS
AF:
0.163
Gnomad4 FIN
AF:
0.232
Gnomad4 NFE
AF:
0.275
Gnomad4 OTH
AF:
0.284
Alfa
AF:
0.292
Hom.:
1199
Bravo
AF:
0.308
Asia WGS
AF:
0.294
AC:
1019
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.8
DANN
Benign
0.35

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: rs7631349; hg19: chr3-81623527; API