rs4643
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002633.3(PGM1):c.*93A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 949,000 control chromosomes in the GnomAD database, including 18,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 2651 hom., cov: 32)
Exomes 𝑓: 0.19 ( 16226 hom. )
Consequence
PGM1
NM_002633.3 3_prime_UTR
NM_002633.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.192
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 1-63659768-A-C is Benign according to our data. Variant chr1-63659768-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 297897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGM1 | NM_002633.3 | c.*93A>C | 3_prime_UTR_variant | 11/11 | ENST00000371084.8 | ||
PGM1 | NM_001172818.1 | c.*93A>C | 3_prime_UTR_variant | 11/11 | |||
PGM1 | NM_001172819.2 | c.*93A>C | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGM1 | ENST00000371084.8 | c.*93A>C | 3_prime_UTR_variant | 11/11 | 1 | NM_002633.3 | P1 | ||
PGM1 | ENST00000371083.4 | c.*93A>C | 3_prime_UTR_variant | 11/11 | 2 | ||||
PGM1 | ENST00000540265.5 | c.*93A>C | 3_prime_UTR_variant | 11/11 | 2 | ||||
PGM1 | ENST00000650546.1 | c.*149A>C | 3_prime_UTR_variant | 12/12 |
Frequencies
GnomAD3 genomes ? AF: 0.174 AC: 26500AN: 152054Hom.: 2651 Cov.: 32
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GnomAD4 exome AF: 0.195 AC: 155065AN: 796828Hom.: 16226 Cov.: 11 AF XY: 0.194 AC XY: 80979AN XY: 418038
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GnomAD4 genome ? AF: 0.174 AC: 26519AN: 152172Hom.: 2651 Cov.: 32 AF XY: 0.179 AC XY: 13350AN XY: 74386
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 38% of patients studied by a panel of primary immunodeficiencies. Number of patients: 36. Only high quality variants are reported. - |
Congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | - - |
PGM1-congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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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