Variant 6-83191204-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001199917.2(PGM3):c.65T>A(p.Val22Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00947 in 1,534,568 control chromosomes in the GnomAD database, including 494 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 164 hom., cov: 32)

Exomes 𝑓: 0.0073 ( 330 hom. )

Consequence

PGM3
NM_001199917.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0380

Variant links:

Genes affected

PGM3 (HGNC:8907): (phosphoglucomutase 3) This gene encodes a member of the phosphohexose mutase family. The encoded protein mediates both glycogen formation and utilization by catalyzing the interconversion of glucose-1-phosphate and glucose-6-phosphate. A non-synonymous single nucleotide polymorphism in this gene may play a role in resistance to diabetic nephropathy and neuropathy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

PGM3 links:

PGM3 (HGNC:):

PGM3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019480586).

BP6

Variant 6-83191204-A-T is Benign according to our data. Variant chr6-83191204-A-T is described in ClinVar as [Benign]. Clinvar id is 475004.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGM3	NM_015599.3 linkuse as main transcript	c.-2-190T>A		intron_variant		ENST00000513973.6	NP_056414.1	O95394-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGM3	ENST00000513973.6 linkuse as main transcript	c.-2-190T>A		intron_variant		1	NM_015599.3	ENSP00000424874.1		O95394-1
PGM3	ENST00000283977.9 linkuse as main transcript	c.-40+1975T>A		intron_variant		5		ENSP00000283977.5		J3KN95

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4490

AN:

151994

Hom.:

160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0811

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0271

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0838

Gnomad SAS

AF:

0.0358

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.000750

Gnomad OTH

AF:

0.0258

GnomAD3 exomes

AF:

0.0202

AC:

2637

AN:

130380

Hom.:

AF XY:

0.0204

AC XY:

1447

AN XY:

71080

show subpopulations

Gnomad AFR exome

AF:

0.0900

Gnomad AMR exome

AF:

0.0134

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0830

Gnomad SAS exome

AF:

0.0341

Gnomad FIN exome

AF:

0.000368

Gnomad NFE exome

AF:

0.000983

Gnomad OTH exome

AF:

0.00870

GnomAD4 exome

AF:

0.00725

AC:

10023

AN:

1382456

Hom.:

330

Cov.:

AF XY:

0.00785

AC XY:

5357

AN XY:

682220

show subpopulations

Gnomad4 AFR exome

AF:

0.0870

Gnomad4 AMR exome

AF:

0.0153

Gnomad4 ASJ exome

AF:

0.0000397

Gnomad4 EAS exome

AF:

0.0686

Gnomad4 SAS exome

AF:

0.0330

Gnomad4 FIN exome

AF:

0.000418

Gnomad4 NFE exome

AF:

0.000709

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0296

AC:

4502

AN:

152112

Hom.:

164

Cov.:

AF XY:

0.0300

AC XY:

2228

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0811

Gnomad4 AMR

AF:

0.0270

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0839

Gnomad4 SAS

AF:

0.0359

Gnomad4 FIN

AF:

0.000566

Gnomad4 NFE

AF:

0.000750

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.00481

Hom.:

Bravo

AF:

0.0327

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00

AC:

ExAC

AF:

0.0107

AC:

461

Asia WGS

AF:

0.0620

AC:

214

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2020

- -

Immunodeficiency 23

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.58

CADD

Benign

1.5

DANN

Benign

0.56

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.47

T;T;T

MetaRNN

Benign

0.0019

T;T;T

MetaSVM

Benign

-0.99

PrimateAI

Benign

0.35

PROVEAN

Benign

0.34

N;N;N

REVEL

Benign

0.076

Sift

Pathogenic

0.0

D;D;D

Sift4G

Uncertain

0.0050

D;.;D

Vest4

0.069

MPC

0.32

ClinPred

0.0050

GERP RS

-0.79

gMVP

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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