rs77043134

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 8P and 16B. PVS1BP6_Very_StrongBS1BS2

The NM_001172818.1(PGM1):c.300+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,602,052 control chromosomes in the GnomAD database, including 156 homozygotes. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 24 hom., cov: 32)

Exomes 𝑓: 0.013 ( 132 hom. )

Consequence

PGM1
NM_001172818.1 splice_donor, intron

Scores

Splicing: ADA: 1.000

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 9.56

Variant links:

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]

PGM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.

BP6

Variant 1-63623761-G-A is Benign according to our data. Variant chr1-63623761-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 445924.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-63623761-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0102 (1552/152262) while in subpopulation NFE AF= 0.0167 (1133/68026). AF 95% confidence interval is 0.0158. There are 24 homozygotes in gnomad4. There are 662 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PGM1	NM_002633.3 link	c.247-5664G>A	intron_variant	Intron 1 of 10	ENST00000371084.8	NP_002624.2	P36871-1
PGM1	NM_001172818.1 link	c.300+1G>A	splice_donor_variant, intron_variant	Intron 1 of 10		NP_001166289.1	P36871-2B7Z6C2
PGM1	NM_001172819.2 link	c.-345-5664G>A	intron_variant	Intron 1 of 10		NP_001166290.1	P36871-3B4DDQ8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PGM1	ENST00000371084.8 link	c.247-5664G>A	intron_variant	Intron 1 of 10	1	NM_002633.3	ENSP00000360125.3	P36871-1
PGM1	ENST00000650546.1 link	c.247-5664G>A	intron_variant	Intron 1 of 11			ENSP00000497812.1	A0A3B3ITK7
PGM1	ENST00000371083.4 link	c.300+1G>A	splice_donor_variant, intron_variant	Intron 1 of 10	2		ENSP00000360124.4	P36871-2
PGM1	ENST00000540265.5 link	c.-345-5664G>A	intron_variant	Intron 1 of 10	2		ENSP00000443449.1	P36871-3

Frequencies

GnomAD3 genomes

AF:

0.0102

AC:

1552

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00266

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00434

Gnomad FIN

AF:

0.00641

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0167

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00931

AC:

2223

AN:

238772

Hom.:

AF XY:

0.00950

AC XY:

1246

AN XY:

131174

show subpopulations

Gnomad AFR exome

AF:

0.00197

Gnomad AMR exome

AF:

0.00278

Gnomad ASJ exome

AF:

0.0207

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.00253

Gnomad FIN exome

AF:

0.00749

Gnomad NFE exome

AF:

0.0152

Gnomad OTH exome

AF:

0.00864

GnomAD4 exome

AF:

0.0128

AC:

18533

AN:

1449790

Hom.:

132

Cov.:

AF XY:

0.0126

AC XY:

9119

AN XY:

721556

show subpopulations

Gnomad4 AFR exome

AF:

0.00211

Gnomad4 AMR exome

AF:

0.00326

Gnomad4 ASJ exome

AF:

0.0185

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.00291

Gnomad4 FIN exome

AF:

0.00816

Gnomad4 NFE exome

AF:

0.0150

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.0102

AC:

1552

AN:

152262

Hom.:

Cov.:

AF XY:

0.00889

AC XY:

662

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00265

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.0190

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00435

Gnomad4 FIN

AF:

0.00641

Gnomad4 NFE

AF:

0.0167

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.0145

Hom.:

Bravo

AF:

0.00931

TwinsUK

AF:

0.0167

AC:

ALSPAC

AF:

0.0130

AC:

ESP6500AA

AF:

0.00228

AC:

ESP6500EA

AF:

0.0136

AC:

ExAC

AF:

0.00981

AC:

1137

Asia WGS

AF:

0.00144

AC:

AN:

3476

EpiCase

AF:

0.0134

EpiControl

AF:

0.0122

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:6

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 26, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 32552793, 28820871, 27124789) -

Sep 01, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PGM1: BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

PGM1-congenital disorder of glycosylation

Benign:2

Jan 06, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 09, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.080

BayesDel_noAF

Pathogenic

0.36

CADD

Benign

DANN

Uncertain

1.0

Eigen

Pathogenic

1.2

Eigen_PC

Pathogenic

1.0

FATHMM_MKL

Pathogenic

0.99

GERP RS

5.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.94

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over