chr19-48970169-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002103.5(GYS1):c.1810-314C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 479,504 control chromosomes in the GnomAD database, including 686 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.044 ( 216 hom., cov: 32)
Exomes 𝑓: 0.047 ( 470 hom. )
Consequence
GYS1
NM_002103.5 intron
NM_002103.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.838
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0613 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS1 | NM_002103.5 | c.1810-314C>T | intron_variant | ENST00000323798.8 | |||
GYS1 | NM_001161587.2 | c.1618-314C>T | intron_variant | ||||
GYS1 | NR_027763.2 | n.1825-314C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS1 | ENST00000323798.8 | c.1810-314C>T | intron_variant | 1 | NM_002103.5 | P1 | |||
GYS1 | ENST00000263276.6 | c.1618-314C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0444 AC: 6748AN: 151976Hom.: 214 Cov.: 32
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GnomAD4 exome AF: 0.0466 AC: 15248AN: 327410Hom.: 470 AF XY: 0.0451 AC XY: 7799AN XY: 173082
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GnomAD4 genome AF: 0.0444 AC: 6756AN: 152094Hom.: 216 Cov.: 32 AF XY: 0.0479 AC XY: 3561AN XY: 74344
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at