3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTG

Position:

• chr3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_004130.4(GYG1):​c.481+176_481+179dupGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 606,590 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0025 (6 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]

GYG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00252 (1150/456772) while in subpopulation AFR AF= 0.00695 (89/12810). AF 95% confidence interval is 0.00578. There are 6 homozygotes in gnomad4_exome. There are 643 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+176_481+179dupGTGT		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+176_481+179dupGTGT		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+176_481+179dupGTGT		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+176_304+179dupGTGT		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+179dupGTGT		intron_variant		1	NM_004130.4	ENSP00000340736.4

Frequencies

GnomAD3 genomes AF: 0.00209 AC: 313 AN: 149702 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000266

Gnomad ASJ AF: 0.0139

Gnomad EAS AF: 0.00234

Gnomad SAS AF: 0.00233

Gnomad FIN AF: 0.000884

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00191

Gnomad OTH AF: 0.00245

GnomAD4 exome AF: 0.00252 AC: 1150 AN: 456772 Hom.: 6 AF XY: 0.00264 AC XY: 643 AN XY: 243786

Gnomad4 AFR exome AF: 0.00695

Gnomad4 AMR exome AF: 0.000789

Gnomad4 ASJ exome AF: 0.0116

Gnomad4 EAS exome AF: 0.000865

Gnomad4 SAS exome AF: 0.00314

Gnomad4 FIN exome AF: 0.000971

Gnomad4 NFE exome AF: 0.00214

Gnomad4 OTH exome AF: 0.00305

GnomAD4 genome AF: 0.00209 AC: 313 AN: 149818 Hom.: 0 Cov.: 0 AF XY: 0.00192 AC XY: 140 AN XY: 73098

Gnomad4 AFR AF: 0.00234

Gnomad4 AMR AF: 0.000266

Gnomad4 ASJ AF: 0.0139

Gnomad4 EAS AF: 0.00234

Gnomad4 SAS AF: 0.00233

Gnomad4 FIN AF: 0.000884

Gnomad4 NFE AF: 0.00191

Gnomad4 OTH AF: 0.00242

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;