Variant 4-37834613-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_018290.4(PGM2):c.250-5T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,395,466 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 25 hom. )

Consequence

PGM2
NM_018290.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001654

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.58

Variant links:

Genes affected

PGM2 (HGNC:8906): (phosphoglucomutase 2) Enables phosphopentomutase activity. Predicted to be involved in carbohydrate metabolic process and deoxyribose phosphate catabolic process. Predicted to act upstream of or within glucose metabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

PGM2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 4-37834613-T-C is Benign according to our data. Variant chr4-37834613-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2654719.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2	NM_018290.4 linkuse as main transcript	c.250-5T>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000381967.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2	ENST00000381967.9 linkuse as main transcript	c.250-5T>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_018290.4	P1	Q96G03-1

Frequencies

GnomAD3 genomes

AF:

0.00258

AC:

392

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000917

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00372

Gnomad FIN

AF:

0.00527

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00413

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00263

AC:

640

AN:

243738

Hom.:

AF XY:

0.00291

AC XY:

383

AN XY:

131798

show subpopulations

Gnomad AFR exome

AF:

0.000254

Gnomad AMR exome

AF:

0.000434

Gnomad ASJ exome

AF:

0.00214

Gnomad EAS exome

AF:

0.0000561

Gnomad SAS exome

AF:

0.00472

Gnomad FIN exome

AF:

0.00348

Gnomad NFE exome

AF:

0.00331

Gnomad OTH exome

AF:

0.00322

GnomAD4 exome

AF:

0.00271

AC:

3372

AN:

1243122

Hom.:

Cov.:

AF XY:

0.00292

AC XY:

1839

AN XY:

629474

show subpopulations

Gnomad4 AFR exome

AF:

0.000141

Gnomad4 AMR exome

AF:

0.000591

Gnomad4 ASJ exome

AF:

0.00183

Gnomad4 EAS exome

AF:

0.0000260

Gnomad4 SAS exome

AF:

0.00510

Gnomad4 FIN exome

AF:

0.00438

Gnomad4 NFE exome

AF:

0.00277

Gnomad4 OTH exome

AF:

0.00178

GnomAD4 genome

AF:

0.00258

AC:

393

AN:

152344

Hom.:

Cov.:

AF XY:

0.00255

AC XY:

190

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.000265

Gnomad4 AMR

AF:

0.000915

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00393

Gnomad4 FIN

AF:

0.00527

Gnomad4 NFE

AF:

0.00413

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00355

Hom.:

Bravo

AF:

0.00159

Asia WGS

AF:

0.00231

AC:

AN:

3472

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

PGM2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.4

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0017

dbscSNV1_RF

Benign

0.034

SpliceAI score (max)

0.020

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