3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTG

Position:

• chr3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTG

Variant summary

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

The NM_004130.4(GYG1):​c.481+176_481+179delGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 596,190 control chromosomes in the GnomAD database, including 15,635 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (8498 hom., cov: 0)
  • Exomes 𝑓: 0.29 (7137 hom.)
• Consequence: GYG1 NM_004130.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.76

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-TTGTG-T is Benign according to our data. Variant chr3-148997054-TTGTG-T is described in ClinVar as [Benign]. Clinvar id is 1263024.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+176_481+179delGTGT		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+176_481+179delGTGT		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+176_481+179delGTGT		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+176_304+179delGTGT		intron_variant			XP_016861764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GYG1	ENST00000345003.9	c.481+176_481+179delGTGT		intron_variant		1	NM_004130.4	ENSP00000340736.4

Frequencies

GnomAD3 genomes AF: 0.340 AC: 50767 AN: 149478 Hom.: 8495 Cov.: 0

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.289 AC: 128892 AN: 446598 Hom.: 7137 AF XY: 0.283 AC XY: 67519 AN XY: 238448

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.274

Gnomad4 ASJ exome AF: 0.308

Gnomad4 EAS exome AF: 0.319

Gnomad4 SAS exome AF: 0.239

Gnomad4 FIN exome AF: 0.351

Gnomad4 NFE exome AF: 0.286

Gnomad4 OTH exome AF: 0.298

GnomAD4 genome AF: 0.340 AC: 50799 AN: 149592 Hom.: 8498 Cov.: 0 AF XY: 0.340 AC XY: 24793 AN XY: 72956

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.337

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

Sep 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs10571382; hg19: chr3-148714841;