Genetic Variant GYG1:c.481+170_481+179dupGTGTGTGTGT (chr3-148997054-T-TTGTGTGTGTG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_004130.4(GYG1):c.481+170_481+179dupGTGTGTGTGT 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.285

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 0 ACMG points.

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+170_481+179dupGTGTGTGTGT	intron	N/A	NP_004121.2
GYG1	NM_001184720.2		c.481+170_481+179dupGTGTGTGTGT	intron	N/A	NP_001171649.1
GYG1	NM_001184721.2		c.481+170_481+179dupGTGTGTGTGT	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+150_481+151insTGTGTGTGTG	intron	N/A	ENSP00000340736.4
GYG1	ENST00000296048.10	TSL:1	c.481+150_481+151insTGTGTGTGTG	intron	N/A	ENSP00000296048.6
GYG1	ENST00000484197.5	TSL:1	c.481+150_481+151insTGTGTGTGTG	intron	N/A	ENSP00000420683.1

Frequencies

GnomAD3 genomes

AF:

0.000655

AC:

AN:

149704

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.000611

AC XY:

149

AN XY:

243884

show subpopulations

African (AFR)

AF:

0.00124

AC:

AN:

12856

American (AMR)

AF:

0.000291

AC:

AN:

24088

Ashkenazi Jewish (ASJ)

AF:

0.00387

AC:

AN:

14716

East Asian (EAS)

AF:

0.00

AC:

AN:

28888

South Asian (SAS)

AF:

0.000580

AC:

AN:

50006

European-Finnish (FIN)

AF:

0.0000693

AC:

AN:

28848

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2106

European-Non Finnish (NFE)

AF:

0.000523

AC:

141

AN:

269578

Other (OTH)

AF:

0.00112

AC:

AN:

25920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.416

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:

0.000674

AC:

101

AN:

149820

Hom.:

Cov.:

AF XY:

0.000643

AC XY:

AN XY:

73098

show subpopulations

African (AFR)

AF:

0.000886

AC:

AN:

40632

American (AMR)

AF:

0.000532

AC:

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.00550

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:

0.000564

AC:

AN:

67416

Other (OTH)

AF:

0.00

AC:

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.28

Splicing

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

Publications

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3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over