rs41317304
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002863.5(PYGL):c.529-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 1,610,916 control chromosomes in the GnomAD database, including 1,719 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.059 ( 379 hom., cov: 32)
Exomes 𝑓: 0.038 ( 1340 hom. )
Consequence
PYGL
NM_002863.5 intron
NM_002863.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.519
Genes affected
PYGL (HGNC:9725): (glycogen phosphorylase L) This gene encodes a homodimeric protein that catalyses the cleavage of alpha-1,4-glucosidic bonds to release glucose-1-phosphate from liver glycogen stores. This protein switches from inactive phosphorylase B to active phosphorylase A by phosphorylation of serine residue 15. Activity of this enzyme is further regulated by multiple allosteric effectors and hormonal controls. Humans have three glycogen phosphorylase genes that encode distinct isozymes that are primarily expressed in liver, brain and muscle, respectively. The liver isozyme serves the glycemic demands of the body in general while the brain and muscle isozymes supply just those tissues. In glycogen storage disease type VI, also known as Hers disease, mutations in liver glycogen phosphorylase inhibit the conversion of glycogen to glucose and results in moderate hypoglycemia, mild ketosis, growth retardation and hepatomegaly. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Feb 2011]
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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 14-50924122-C-T is Benign according to our data. Variant chr14-50924122-C-T is described in ClinVar as [Benign]. Clinvar id is 258845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PYGL | NM_002863.5 | c.529-22G>A | intron_variant | ENST00000216392.8 | |||
PYGL | NM_001163940.2 | c.427-22G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PYGL | ENST00000216392.8 | c.529-22G>A | intron_variant | 1 | NM_002863.5 | P1 | |||
PYGL | ENST00000532462.5 | c.529-22G>A | intron_variant | 1 | |||||
PYGL | ENST00000530336.2 | n.596-22G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
PYGL | ENST00000544180.6 | c.427-22G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0589 AC: 8961AN: 152056Hom.: 377 Cov.: 32
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GnomAD3 exomes AF: 0.0403 AC: 10123AN: 251058Hom.: 306 AF XY: 0.0402 AC XY: 5453AN XY: 135702
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GnomAD4 exome AF: 0.0383 AC: 55829AN: 1458742Hom.: 1340 Cov.: 30 AF XY: 0.0384 AC XY: 27870AN XY: 725874
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GnomAD4 genome ? AF: 0.0589 AC: 8965AN: 152174Hom.: 379 Cov.: 32 AF XY: 0.0587 AC XY: 4369AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 21, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 12, 2017 | - - |
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