3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTG

Position:

• chr3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004130.4(GYG1):​c.481+170_481+179dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00063 in 606,826 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00067 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00061 (0 hom.)
• Consequence: GYG1 NM_004130.4 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+170_481+179dup		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+170_481+179dup		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+170_481+179dup		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+170_304+179dup		intron_variant			XP_016861764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GYG1	ENST00000345003.9	c.481+170_481+179dup		intron_variant		1	NM_004130.4	ENSP00000340736

Frequencies

GnomAD3 genomes AF: 0.000655 AC: 98 AN: 149704 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000815

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000532

Gnomad ASJ AF: 0.00550

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000564

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000615 AC: 281 AN: 457006 Hom.: 0 AF XY: 0.000611 AC XY: 149 AN XY: 243884

Gnomad4 AFR exome AF: 0.00124

Gnomad4 AMR exome AF: 0.000291

Gnomad4 ASJ exome AF: 0.00387

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000580

Gnomad4 FIN exome AF: 0.0000693

Gnomad4 NFE exome AF: 0.000523

Gnomad4 OTH exome AF: 0.00112

GnomAD4 genome AF: 0.000674 AC: 101 AN: 149820 Hom.: 0 Cov.: 0 AF XY: 0.000643 AC XY: 47 AN XY: 73098

Gnomad4 AFR AF: 0.000886

Gnomad4 AMR AF: 0.000532

Gnomad4 ASJ AF: 0.00550

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000564

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;