3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTG

Position:

• chr3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTG

Variant summary

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

The NM_004130.4(GYG1):​c.481+174_481+179dupGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 606,324 control chromosomes in the GnomAD database, including 191 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.032 (167 hom., cov: 0)
  • Exomes 𝑓: 0.011 (24 hom.)
• Consequence: GYG1 NM_004130.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.285

Genes affected

GYG1 (HGNC:4699): (glycogenin 1) This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and branching of the polymer, catalyzed by glycogen synthase and branching enzyme, to form glycogen. This gene is expressed in muscle and other tissues. Mutations in this gene result in glycogen storage disease XV. This gene has pseudogenes on chromosomes 1, 8 and 13 respectively. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

GYG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-148997054-T-TTGTGTG is Benign according to our data. Variant chr3-148997054-T-TTGTGTG is described in ClinVar as [Benign]. Clinvar id is 1265049.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+174_481+179dupGTGTGT		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+174_481+179dupGTGTGT		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+174_481+179dupGTGTGT		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+174_304+179dupGTGTGT		intron_variant			XP_016861764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GYG1	ENST00000345003.9	c.481+174_481+179dupGTGTGT		intron_variant		1	NM_004130.4	ENSP00000340736.4

Frequencies

GnomAD3 genomes AF: 0.0318 AC: 4760 AN: 149668 Hom.: 168 Cov.: 0

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.00579

Gnomad EAS AF: 0.000780

Gnomad SAS AF: 0.00593

Gnomad FIN AF: 0.00246

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0240

GnomAD4 exome AF: 0.0113 AC: 5151 AN: 456542 Hom.: 24 AF XY: 0.0109 AC XY: 2646 AN XY: 243636

Gnomad4 AFR exome AF: 0.0797

Gnomad4 AMR exome AF: 0.0107

Gnomad4 ASJ exome AF: 0.00517

Gnomad4 EAS exome AF: 0.0000692

Gnomad4 SAS exome AF: 0.00619

Gnomad4 FIN exome AF: 0.00403

Gnomad4 NFE exome AF: 0.0110

Gnomad4 OTH exome AF: 0.0151

GnomAD4 genome AF: 0.0319 AC: 4776 AN: 149782 Hom.: 167 Cov.: 0 AF XY: 0.0299 AC XY: 2182 AN XY: 73082

Gnomad4 AFR AF: 0.0893

Gnomad4 AMR AF: 0.0187

Gnomad4 ASJ AF: 0.00579

Gnomad4 EAS AF: 0.000782

Gnomad4 SAS AF: 0.00573

Gnomad4 FIN AF: 0.00246

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0233

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

Oct 25, 2020

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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: rs10571382; hg19: chr3-148714841;