rs1042265
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002103.5(GYS1):c.*725C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 454,382 control chromosomes in the GnomAD database, including 2,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.097 ( 763 hom., cov: 32)
Exomes 𝑓: 0.094 ( 1499 hom. )
Consequence
GYS1
NM_002103.5 3_prime_UTR
NM_002103.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.153
Genes affected
GYS1 (HGNC:4706): (glycogen synthase 1) The protein encoded by this gene catalyzes the addition of glucose monomers to the growing glycogen molecule through the formation of alpha-1,4-glycoside linkages. Mutations in this gene are associated with muscle glycogen storage disease. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 19-48968563-G-A is Benign according to our data. Variant chr19-48968563-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 329796.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS1 | NM_002103.5 | c.*725C>T | 3_prime_UTR_variant | 16/16 | ENST00000323798.8 | ||
GYS1 | NM_001161587.2 | c.*725C>T | 3_prime_UTR_variant | 15/15 | |||
GYS1 | NR_027763.2 | n.2954C>T | non_coding_transcript_exon_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS1 | ENST00000323798.8 | c.*725C>T | 3_prime_UTR_variant | 16/16 | 1 | NM_002103.5 | P1 | ||
GYS1 | ENST00000263276.6 | c.*725C>T | 3_prime_UTR_variant | 15/15 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0970 AC: 14754AN: 152066Hom.: 763 Cov.: 32
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GnomAD3 exomes AF: 0.0989 AC: 13477AN: 136236Hom.: 771 AF XY: 0.0933 AC XY: 6905AN XY: 74030
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GnomAD4 exome AF: 0.0940 AC: 28417AN: 302198Hom.: 1499 Cov.: 0 AF XY: 0.0893 AC XY: 15384AN XY: 172246
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GnomAD4 genome ? AF: 0.0970 AC: 14765AN: 152184Hom.: 763 Cov.: 32 AF XY: 0.0947 AC XY: 7044AN XY: 74392
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hereditary hyperferritinemia with congenital cataracts Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Neuroferritinopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Glycogen storage disease due to muscle and heart glycogen synthase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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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