rs34988523

Positions:

• chr3-81499058-T-TAAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000158.4(GBE1):​c.2052+51_2052+52insCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (7325 hom., cov: 0)
  • Exomes 𝑓: 0.27 (30141 hom.)
• Consequence: GBE1 NM_000158.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.33

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 -10 ACMG points.

• BP6: Variant 3-81499058-T-TAAG is Benign according to our data. Variant chr3-81499058-T-TAAG is described in ClinVar as [Benign]. Clinvar id is 1252855.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GBE1	NM_000158.4	c.2052+51_2052+52insCTT		intron_variant		ENST00000429644.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GBE1	ENST00000429644.7	c.2052+51_2052+52insCTT		intron_variant		1	NM_000158.4	P1
GBE1	ENST00000489715.1	c.1929+51_1929+52insCTT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46162 AN: 151608 Hom.: 7315 Cov.: 0

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.267 AC: 214163 AN: 803460 Hom.: 30141 Cov.: 11 AF XY: 0.261 AC XY: 108959 AN XY: 416880

Gnomad4 AFR exome AF: 0.396

Gnomad4 AMR exome AF: 0.272

Gnomad4 ASJ exome AF: 0.173

Gnomad4 EAS exome AF: 0.383

Gnomad4 SAS exome AF: 0.156

Gnomad4 FIN exome AF: 0.238

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.277

GnomAD4 genome AF: 0.305 AC: 46218 AN: 151726 Hom.: 7325 Cov.: 0 AF XY: 0.299 AC XY: 22199 AN XY: 74122

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.294

Alfa AF: 0.285 Hom.: 655

Bravo AF: 0.316

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34988523; hg19: chr3-81548209;