Variant 11-74346886-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.940-57G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 1,329,062 control chromosomes in the GnomAD database, including 264,319 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 24612 hom., cov: 31)

Exomes 𝑓: 0.63 ( 239707 hom. )

Consequence

PGM2L1
NM_173582.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.334

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 (BayesDel_noAF=-0.93).

BP6

Variant 11-74346886-C-T is Benign according to our data. Variant chr11-74346886-C-T is described in ClinVar as [Benign]. Clinvar id is 1241016.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PGM2L1	NM_173582.6 linkuse as main transcript	c.940-57G>A	intron_variant	ENST00000298198.5
LOC112268078	XR_002957258.2 linkuse as main transcript	n.314+17398C>T	intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4 linkuse as main transcript	c.1003-57G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5 linkuse as main transcript	c.940-57G>A		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82319

AN:

151868

Hom.:

24602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.754

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.805

Gnomad SAS

AF:

0.662

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.631

Gnomad OTH

AF:

0.547

GnomAD4 exome

AF:

0.634

AC:

745686

AN:

1177076

Hom.:

239707

AF XY:

0.634

AC XY:

379960

AN XY:

598984

show subpopulations

Gnomad4 AFR exome

AF:

0.254

Gnomad4 AMR exome

AF:

0.671

Gnomad4 ASJ exome

AF:

0.605

Gnomad4 EAS exome

AF:

0.753

Gnomad4 SAS exome

AF:

0.640

Gnomad4 FIN exome

AF:

0.713

Gnomad4 NFE exome

AF:

0.635

Gnomad4 OTH exome

AF:

0.619

GnomAD4 genome

AF:

0.542

AC:

82353

AN:

151986

Hom.:

24612

Cov.:

AF XY:

0.552

AC XY:

40985

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.267

Gnomad4 AMR

AF:

0.617

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.805

Gnomad4 SAS

AF:

0.664

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.631

Gnomad4 OTH

AF:

0.548

Alfa

AF:

0.566

Hom.:

3823

Bravo

AF:

0.523

Asia WGS

AF:

0.684

AC:

2379

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 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.2

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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