3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTG

Position:

• chr3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTG

Variant summary

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

The NM_004130.4(GYG1):​c.481+178_481+179dupGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 605,964 control chromosomes in the GnomAD database, including 198 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.039 (144 hom., cov: 0)
  • Exomes 𝑓: 0.039 (54 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-148997054-T-TTG is Benign according to our data. Variant chr3-148997054-T-TTG is described in ClinVar as [Benign]. Clinvar id is 1236135.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYG1	NM_004130.4	c.481+178_481+179dupGT		intron_variant		ENST00000345003.9	NP_004121.2
GYG1	NM_001184720.2	c.481+178_481+179dupGT		intron_variant			NP_001171649.1
GYG1	NM_001184721.2	c.481+178_481+179dupGT		intron_variant			NP_001171650.1
GYG1	XM_017006275.2	c.304+178_304+179dupGT		intron_variant			XP_016861764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GYG1	ENST00000345003.9	c.481+150_481+151insTG		intron_variant		1	NM_004130.4	ENSP00000340736.4

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5776 AN: 149686 Hom.: 144 Cov.: 0

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.0348

GnomAD4 exome AF: 0.0390 AC: 17780 AN: 456162 Hom.: 54 AF XY: 0.0394 AC XY: 9591 AN XY: 243444

Gnomad4 AFR exome AF: 0.0152

Gnomad4 AMR exome AF: 0.0239

Gnomad4 ASJ exome AF: 0.0279

Gnomad4 EAS exome AF: 0.0226

Gnomad4 SAS exome AF: 0.0465

Gnomad4 FIN exome AF: 0.0264

Gnomad4 NFE exome AF: 0.0443

Gnomad4 OTH exome AF: 0.0349

GnomAD4 genome AF: 0.0386 AC: 5776 AN: 149802 Hom.: 144 Cov.: 0 AF XY: 0.0375 AC XY: 2737 AN XY: 73084

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.0262

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.0244

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0383

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 08, 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;