rs148619511
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004130.4(GYG1):āc.159A>Gā(p.Thr53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,610,978 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0076 ( 11 hom., cov: 32)
Exomes š: 0.012 ( 147 hom. )
Consequence
GYG1
NM_004130.4 synonymous
NM_004130.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.533
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 3-148996317-A-G is Benign according to our data. Variant chr3-148996317-A-G is described in ClinVar as [Benign]. Clinvar id is 380453.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.533 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00763 (1162/152364) while in subpopulation NFE AF= 0.0129 (879/68034). AF 95% confidence interval is 0.0122. There are 11 homozygotes in gnomad4. There are 515 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYG1 | NM_004130.4 | c.159A>G | p.Thr53= | synonymous_variant | 3/8 | ENST00000345003.9 | |
GYG1 | NM_001184720.2 | c.159A>G | p.Thr53= | synonymous_variant | 3/7 | ||
GYG1 | NM_001184721.2 | c.159A>G | p.Thr53= | synonymous_variant | 3/6 | ||
GYG1 | XM_017006275.2 | c.-19A>G | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYG1 | ENST00000345003.9 | c.159A>G | p.Thr53= | synonymous_variant | 3/8 | 1 | NM_004130.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00763 AC: 1162AN: 152246Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00723 AC: 1817AN: 251224Hom.: 13 AF XY: 0.00683 AC XY: 927AN XY: 135776
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GnomAD4 exome AF: 0.0121 AC: 17690AN: 1458614Hom.: 147 Cov.: 31 AF XY: 0.0118 AC XY: 8562AN XY: 725684
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GnomAD4 genome ? AF: 0.00763 AC: 1162AN: 152364Hom.: 11 Cov.: 32 AF XY: 0.00691 AC XY: 515AN XY: 74526
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | GYG1: BP4, BP7, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 29, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Glycogen storage disease XV;C4015452:Polyglucosan body myopathy type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at