chr3-148997054-TTGTGTG-T

Position:

• chr3-148997054-TTGTGTG-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_004130.4(GYG1):​c.481+174_481+179del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 589,580 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 0.00026 (0 hom., cov: 0)
  • Exomes 𝑓: 0.015 (0 hom.)
• Consequence: GYG1 NM_004130.4 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.015 (6579/439900) while in subpopulation AFR AF= 0.0204 (250/12272). AF 95% confidence interval is 0.0183. There are 0 homozygotes in gnomad4_exome. There are 3422 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+174_481+179del		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+174_481+179del		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+174_481+179del		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+174_304+179del		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+179del		intron_variant		1	NM_004130.4	ENSP00000340736

Frequencies

GnomAD3 genomes AF: 0.000261 AC: 39 AN: 149564 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000866

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000197

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000163

Gnomad OTH AF: 0.000491

GnomAD4 exome AF: 0.0150 AC: 6579 AN: 439900 Hom.: 0 AF XY: 0.0146 AC XY: 3422 AN XY: 234962

Gnomad4 AFR exome AF: 0.0204

Gnomad4 AMR exome AF: 0.0165

Gnomad4 ASJ exome AF: 0.0165

Gnomad4 EAS exome AF: 0.0149

Gnomad4 SAS exome AF: 0.0110

Gnomad4 FIN exome AF: 0.0232

Gnomad4 NFE exome AF: 0.0143

Gnomad4 OTH exome AF: 0.0152

GnomAD4 genome AF: 0.000261 AC: 39 AN: 149680 Hom.: 0 Cov.: 0 AF XY: 0.000219 AC XY: 16 AN XY: 73040

Gnomad4 AFR AF: 0.000295

Gnomad4 AMR AF: 0.000865

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000197

Gnomad4 NFE AF: 0.000163

Gnomad4 OTH AF: 0.000486

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;