chr1-63651866-G-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002633.3(PGM1):c.1464+14G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 1,608,322 control chromosomes in the GnomAD database, including 38,224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5290 hom., cov: 32)

Exomes 𝑓: 0.20 ( 32934 hom. )

Consequence

PGM1
NM_002633.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.206

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 1-63651866-G-T is Benign according to our data. Variant chr1-63651866-G-T is described in ClinVar as [Benign]. Clinvar id is 297890.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
PGM1	NM_002633.3 link	c.1464+14G>T	intron_variant	Intron 9 of 10	ENST00000371084.8	NP_002624.2	P36871-1
PGM1	NM_001172818.1 link	c.1518+14G>T	intron_variant	Intron 9 of 10		NP_001166289.1	P36871-2B7Z6C2
PGM1	NM_001172819.2 link	c.873+14G>T	intron_variant	Intron 9 of 10		NP_001166290.1	P36871-3B4DDQ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGM1	ENST00000371084.8 link	c.1464+14G>T		intron_variant	Intron 9 of 10	1	NM_002633.3	ENSP00000360125.3		P36871-1

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38222

AN:

151924

Hom.:

5272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.238

GnomAD3 exomes

AF:

0.244

AC:

61386

AN:

251084

Hom.:

8742

AF XY:

0.232

AC XY:

31497

AN XY:

135712

show subpopulations

Gnomad AFR exome

AF:

0.325

Gnomad AMR exome

AF:

0.433

Gnomad ASJ exome

AF:

0.160

Gnomad EAS exome

AF:

0.208

Gnomad SAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.316

Gnomad NFE exome

AF:

0.188

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.204

AC:

297666

AN:

1456280

Hom.:

32934

Cov.:

AF XY:

0.202

AC XY:

146729

AN XY:

724750

show subpopulations

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.422

Gnomad4 ASJ exome

AF:

0.163

Gnomad4 EAS exome

AF:

0.191

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.313

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.252

AC:

38297

AN:

152042

Hom.:

5290

Cov.:

AF XY:

0.258

AC XY:

19184

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.327

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.206

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.243

Alfa

AF:

0.178

Hom.:

797

Bravo

AF:

0.258

Asia WGS

AF:

0.219

AC:

761

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Dec 02, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 62% of patients studied by a panel of primary immunodeficiencies. Number of patients: 59. Only high quality variants are reported. -

not provided

Benign:2

Oct 23, 2015

Mayo Clinic Laboratories, Mayo Clinic

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

PGM1-congenital disorder of glycosylation

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Congenital disorder of glycosylation

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.1

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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