rs10511103

chr3-81499441-C-Achr3-81499441-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000158.4(GBE1):c.1935-214G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,264 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.035 (195 hom., cov: 32)
• Consequence: GBE1 NM_000158.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.78

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 3-81499441-C-A is Benign according to our data. Variant chr3-81499441-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1219802.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBE1	NM_000158.4	c.1935-214G>T		intron_variant		ENST00000429644.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBE1	ENST00000429644.7	c.1935-214G>T		intron_variant		1	NM_000158.4	P1
GBE1	ENST00000489715.1	c.1812-214G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5248 AN: 152146 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.00813

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0345 AC: 5257 AN: 152264 Hom.: 195 Cov.: 32 AF XY: 0.0369 AC XY: 2749 AN XY: 74424

Gnomad4 AFR AF: 0.00811

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0110 Hom.: 3

Bravo AF: 0.0392

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.031
Dann	Benign	0.55

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

Other links and lift over

dbSNP: rs10511103; hg19: chr3-81548592;