rs17121560
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000642.3(AGL):c.3260-20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000615 in 1,563,448 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0031 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00034 ( 4 hom. )
Consequence
AGL
NM_000642.3 intron
NM_000642.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.907
Genes affected
AGL (HGNC:321): (amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase) This gene encodes the glycogen debrancher enzyme which is involved in glycogen degradation. This enzyme has two independent catalytic activities which occur at different sites on the protein: a 4-alpha-glucotransferase activity and a amylo-1,6-glucosidase activity. Mutations in this gene are associated with glycogen storage disease although a wide range of enzymatic and clinical variability occurs which may be due to tissue-specific alternative splicing. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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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=-0.54).
BP6
?
Variant 1-99896266-T-C is Benign according to our data. Variant chr1-99896266-T-C is described in ClinVar as [Benign]. Clinvar id is 256737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00313 (477/152340) while in subpopulation AFR AF= 0.0107 (443/41584). AF 95% confidence interval is 0.00983. There are 3 homozygotes in gnomad4. There are 234 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGL | NM_000642.3 | c.3260-20T>C | intron_variant | ENST00000361915.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGL | ENST00000361915.8 | c.3260-20T>C | intron_variant | 1 | NM_000642.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00313 AC: 477AN: 152222Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000879 AC: 221AN: 251412Hom.: 2 AF XY: 0.000633 AC XY: 86AN XY: 135884
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GnomAD4 exome AF: 0.000343 AC: 484AN: 1411108Hom.: 4 Cov.: 26 AF XY: 0.000292 AC XY: 206AN XY: 705190
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GnomAD4 genome ? AF: 0.00313 AC: 477AN: 152340Hom.: 3 Cov.: 33 AF XY: 0.00314 AC XY: 234AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jun 15, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 23, 2018 | This variant is associated with the following publications: (PMID: 20648714) - |
Glycogen storage disease type III Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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