Variant 11-74342502-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_173582.6(PGM2L1):c.1591G>A(p.Val531Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 1,580,536 control chromosomes in the GnomAD database, including 391,900 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.72 ( 39869 hom., cov: 32)

Exomes 𝑓: 0.70 ( 352031 hom. )

Consequence

PGM2L1
NM_173582.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.63

Variant links:

Genes affected

PGM2L1 (HGNC:20898): (phosphoglucomutase 2 like 1) Enables glucose-1,6-bisphosphate synthase activity. Predicted to be involved in glucose metabolic process and phosphorylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

PGM2L1 links:

LOC112268078 (HGNC:):

LOC112268078 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.6870666E-7).

BP6

Variant 11-74342502-C-T is Benign according to our data. Variant chr11-74342502-C-T is described in ClinVar as [Benign]. Clinvar id is 1238287.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PGM2L1	NM_173582.6 linkuse as main transcript	c.1591G>A	p.Val531Ile	missense_variant	12/14	ENST00000298198.5
LOC112268078	XR_002957258.2 linkuse as main transcript	n.314+13014C>T		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4 linkuse as main transcript	c.1654G>A	p.Val552Ile	missense_variant	13/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5 linkuse as main transcript	c.1591G>A	p.Val531Ile	missense_variant	12/14	1	NM_173582.6	P1

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109736

AN:

151974

Hom.:

39815

Cov.:

show subpopulations

Gnomad AFR

AF:

0.761

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.732

Gnomad FIN

AF:

0.759

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.703

GnomAD3 exomes

AF:

0.717

AC:

165563

AN:

231062

Hom.:

59768

AF XY:

0.713

AC XY:

89215

AN XY:

125214

show subpopulations

Gnomad AFR exome

AF:

0.769

Gnomad AMR exome

AF:

0.726

Gnomad ASJ exome

AF:

0.696

Gnomad EAS exome

AF:

0.812

Gnomad SAS exome

AF:

0.708

Gnomad FIN exome

AF:

0.753

Gnomad NFE exome

AF:

0.688

Gnomad OTH exome

AF:

0.709

GnomAD4 exome

AF:

0.701

AC:

1001138

AN:

1428446

Hom.:

352031

Cov.:

AF XY:

0.701

AC XY:

496842

AN XY:

709092

show subpopulations

Gnomad4 AFR exome

AF:

0.768

Gnomad4 AMR exome

AF:

0.726

Gnomad4 ASJ exome

AF:

0.694

Gnomad4 EAS exome

AF:

0.769

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.751

Gnomad4 NFE exome

AF:

0.692

Gnomad4 OTH exome

AF:

0.710

GnomAD4 genome

AF:

0.722

AC:

109851

AN:

152090

Hom.:

39869

Cov.:

AF XY:

0.726

AC XY:

53920

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.761

Gnomad4 AMR

AF:

0.708

Gnomad4 ASJ

AF:

0.698

Gnomad4 EAS

AF:

0.808

Gnomad4 SAS

AF:

0.734

Gnomad4 FIN

AF:

0.759

Gnomad4 NFE

AF:

0.689

Gnomad4 OTH

AF:

0.707

Alfa

AF:

0.698

Hom.:

62983

Bravo

AF:

0.719

TwinsUK

AF:

0.699

AC:

2593

ALSPAC

AF:

0.675

AC:

2603

ESP6500AA

AF:

0.764

AC:

3361

ESP6500EA

AF:

0.689

AC:

5917

ExAC

AF:

0.715

AC:

86744

Asia WGS

AF:

0.753

AC:

2620

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.13

DANN

Benign

0.88

DEOGEN2

Benign

0.020

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.020

LIST_S2

Benign

0.68

MetaRNN

Benign

6.7e-7

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.93

MutationTaster

Benign

1.0

PrimateAI

Benign

0.33

PROVEAN

Benign

0.62

REVEL

Benign

0.080

Sift

Benign

0.090

Sift4G

Uncertain

0.047

Polyphen

0.0010

Vest4

0.016

MPC

0.46

ClinPred

0.0026

GERP RS

-5.5

Varity_R

0.023

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

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