Genetic Variant GYG1:c.481+172_481+179delGTGTGTGT (chr3-148997054-TTGTGTGTG-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_004130.4(GYG1):c.481+172_481+179delGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000495 in 606,478 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000027 ( 1 hom., cov: 0)

Exomes 𝑓: 0.000057 ( 0 hom. )

Consequence

GYG1
NM_004130.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76

Publications

1 publications found

Variant links:

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 Gene-Disease associations (from GenCC):

polyglucosan body myopathy type 2
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, PanelApp Australia, ClinGen
glycogen storage disease XV
Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

GYG1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004130.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GYG1	NM_004130.4	MANE Select	c.481+172_481+179delGTGTGTGT	intron	N/A	NP_004121.2
GYG1	NM_001184720.2		c.481+172_481+179delGTGTGTGT	intron	N/A	NP_001171649.1
GYG1	NM_001184721.2		c.481+172_481+179delGTGTGTGT	intron	N/A	NP_001171650.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GYG1	ENST00000345003.9	TSL:1 MANE Select	c.481+151_481+158delTGTGTGTG	intron	N/A	ENSP00000340736.4
GYG1	ENST00000296048.10	TSL:1	c.481+151_481+158delTGTGTGTG	intron	N/A	ENSP00000296048.6
GYG1	ENST00000484197.5	TSL:1	c.481+151_481+158delTGTGTGTG	intron	N/A	ENSP00000420683.1

Frequencies

GnomAD3 genomes

AF:

0.00000668

AC:

AN:

149700

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000247

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000569

AC:

AN:

456662

Hom.:

AF XY:

0.0000656

AC XY:

AN XY:

243730

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

12852

American (AMR)

AF:

0.0000416

AC:

AN:

24064

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14690

East Asian (EAS)

AF:

0.00

AC:

AN:

28866

South Asian (SAS)

AF:

0.0000200

AC:

AN:

49996

European-Finnish (FIN)

AF:

0.0000347

AC:

AN:

28804

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2104

European-Non Finnish (NFE)

AF:

0.0000817

AC:

AN:

269382

Other (OTH)

AF:

0.0000386

AC:

AN:

25904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.406

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000267

AC:

AN:

149816

Hom.:

Cov.:

AF XY:

0.0000274

AC XY:

AN XY:

73098

show subpopulations

African (AFR)

AF:

0.0000246

AC:

AN:

40630

American (AMR)

AF:

0.00

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3452

East Asian (EAS)

AF:

0.00

AC:

AN:

5118

South Asian (SAS)

AF:

0.00

AC:

AN:

4716

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10182

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67414

Other (OTH)

AF:

0.00145

AC:

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over