rs112502842
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002633.3(PGM1):c.573G>A(p.Ser191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000681 in 1,613,330 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0035 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 3 hom. )
Consequence
PGM1
NM_002633.3 synonymous
NM_002633.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.84
Genes affected
PGM1 (HGNC:8905): (phosphoglucomutase 1) The protein encoded by this gene is an isozyme of phosphoglucomutase (PGM) and belongs to the phosphohexose mutase family. There are several PGM isozymes, which are encoded by different genes and catalyze the transfer of phosphate between the 1 and 6 positions of glucose. In most cell types, this PGM isozyme is predominant, representing about 90% of total PGM activity. In red cells, PGM2 is a major isozyme. This gene is highly polymorphic. Mutations in this gene cause glycogen storage disease type 14. Alternativley spliced transcript variants encoding different isoforms have been identified in this gene.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 1-63631673-G-A is Benign according to our data. Variant chr1-63631673-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 381432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.84 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00354 (539/152226) while in subpopulation AFR AF= 0.0123 (510/41512). AF 95% confidence interval is 0.0114. There are 0 homozygotes in gnomad4. There are 243 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.573G>A | p.Ser191= | synonymous_variant | 4/11 | ENST00000371084.8 | |
PGM1 | NM_001172818.1 | c.627G>A | p.Ser209= | synonymous_variant | 4/11 | ||
PGM1 | NM_001172819.2 | c.-19G>A | 5_prime_UTR_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084.8 | c.573G>A | p.Ser191= | synonymous_variant | 4/11 | 1 | NM_002633.3 | P1 | |
PGM1 | ENST00000650546.1 | c.573G>A | p.Ser191= | synonymous_variant | 4/12 | ||||
PGM1 | ENST00000371083.4 | c.627G>A | p.Ser209= | synonymous_variant | 4/11 | 2 | |||
PGM1 | ENST00000540265.5 | c.-19G>A | 5_prime_UTR_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00354 AC: 539AN: 152108Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000972 AC: 244AN: 251020Hom.: 1 AF XY: 0.000715 AC XY: 97AN XY: 135636
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GnomAD4 exome AF: 0.000383 AC: 559AN: 1461104Hom.: 3 Cov.: 30 AF XY: 0.000327 AC XY: 238AN XY: 726912
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GnomAD4 genome ? AF: 0.00354 AC: 539AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00327 AC XY: 243AN XY: 74420
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 08, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 07, 2020 | - - |
PGM1-congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
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