3-148994138-T-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004130.4(GYG1):c.8-4T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
GYG1
NM_004130.4 splice_region, intron
NM_004130.4 splice_region, intron
Scores
2
Splicing: ADA: 0.0003222
2
Clinical Significance
Conservation
PhyloP100: 1.88
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 3-148994138-T-A is Benign according to our data. Variant chr3-148994138-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 3752645.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GYG1 | NM_004130.4 | c.8-4T>A | splice_region_variant, intron_variant | Intron 1 of 7 | ENST00000345003.9 | NP_004121.2 | ||
| GYG1 | NM_001184720.2 | c.8-4T>A | splice_region_variant, intron_variant | Intron 1 of 6 | NP_001171649.1 | |||
| GYG1 | NM_001184721.2 | c.8-4T>A | splice_region_variant, intron_variant | Intron 1 of 5 | NP_001171650.1 | |||
| GYG1 | XM_017006275.2 | c.-34-2164T>A | intron_variant | Intron 1 of 5 | XP_016861764.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461032Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726876
GnomAD4 exome
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2
AN:
1461032
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Cov.:
31
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1
AN XY:
726876
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Bravo
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disease XV;C4015452:Polyglucosan body myopathy type 2 Benign:1
Jan 28, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at