3-148997054-TTGTGTGTGTGTGTG-TTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000345003.9(GYG1):​c.481+170_481+179del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 606,856 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 0.000027 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

GYG1
ENST00000345003.9 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GYG1NM_004130.4 linkuse as main transcriptc.481+170_481+179del intron_variant ENST00000345003.9 NP_004121.2
GYG1NM_001184720.2 linkuse as main transcriptc.481+170_481+179del intron_variant NP_001171649.1
GYG1NM_001184721.2 linkuse as main transcriptc.481+170_481+179del intron_variant NP_001171650.1
GYG1XM_017006275.2 linkuse as main transcriptc.304+170_304+179del intron_variant XP_016861764.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GYG1ENST00000345003.9 linkuse as main transcriptc.481+170_481+179del intron_variant 1 NM_004130.4 ENSP00000340736 P46976-1

Frequencies

GnomAD3 genomes
AF:
0.0000200
AC:
3
AN:
149704
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000195
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000297
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000306
AC:
14
AN:
457036
Hom.:
0
AF XY:
0.0000328
AC XY:
8
AN XY:
243900
show subpopulations
Gnomad4 AFR exome
AF:
0.000155
Gnomad4 AMR exome
AF:
0.0000415
Gnomad4 ASJ exome
AF:
0.0000679
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000800
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000223
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000267
AC:
4
AN:
149820
Hom.:
0
Cov.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
73098
show subpopulations
Gnomad4 AFR
AF:
0.0000246
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000195
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000297
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10571382; hg19: chr3-148714841; API