GeneBe

rs10571382

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_004130.4(GYG1):​c.481+166_481+179del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00098 in 606,854 control chromosomes in the GnomAD database, including 7 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00085 ( 2 hom., cov: 0)
Exomes 𝑓: 0.0010 ( 5 hom. )

Consequence

GYG1
NM_004130.4 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 Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00102 (468/457038) while in subpopulation MID AF= 0.0161 (34/2106). AF 95% confidence interval is 0.0119. There are 5 homozygotes in gnomad4_exome. There are 259 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GYG1NM_004130.4 linkuse as main transcriptc.481+166_481+179del intron_variant ENST00000345003.9 NP_004121.2
GYG1NM_001184720.2 linkuse as main transcriptc.481+166_481+179del intron_variant NP_001171649.1
GYG1NM_001184721.2 linkuse as main transcriptc.481+166_481+179del intron_variant NP_001171650.1
GYG1XM_017006275.2 linkuse as main transcriptc.304+166_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+166_481+179del intron_variant 1 NM_004130.4 ENSP00000340736 P46976-1

Frequencies

GnomAD3 genomes
AF:
0.000855
AC:
128
AN:
149700
Hom.:
2
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000741
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00266
Gnomad ASJ
AF:
0.00753
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00169
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0318
Gnomad NFE
AF:
0.000564
Gnomad OTH
AF:
0.00147
GnomAD4 exome
AF:
0.00102
AC:
468
AN:
457038
Hom.:
5
AF XY:
0.00106
AC XY:
259
AN XY:
243904
show subpopulations
Gnomad4 AFR exome
AF:
0.000311
Gnomad4 AMR exome
AF:
0.00270
Gnomad4 ASJ exome
AF:
0.00781
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00140
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000519
Gnomad4 OTH exome
AF:
0.00154
GnomAD4 genome
AF:
0.000848
AC:
127
AN:
149816
Hom.:
2
Cov.:
0
AF XY:
0.000862
AC XY:
63
AN XY:
73096
show subpopulations
Gnomad4 AFR
AF:
0.0000738
Gnomad4 AMR
AF:
0.00266
Gnomad4 ASJ
AF:
0.00753
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00148
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000564
Gnomad4 OTH
AF:
0.00145

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