Variant chr9-68378303-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_021965.4(PGM5):c.366C>T(p.Ser122Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 151,324 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 175 hom., cov: 28)

Exomes 𝑓: 0.041 ( 1246 hom. )

Failed GnomAD Quality Control

Consequence

PGM5
NM_021965.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.498

Variant links:

Genes affected

PGM5 (HGNC:8908): (phosphoglucomutase 5) Phosphoglucomutases (EC 5.2.2.2.), such as PGM5, are phosphotransferases involved in interconversion of glucose-1-phosphate and glucose-6-phosphate. PGM activity is essential in formation of carbohydrates from glucose-6-phosphate and in formation of glucose-6-phosphate from galactose and glycogen (Edwards et al., 1995 [PubMed 8586438]).[supplied by OMIM, Mar 2008]

PGM5 links:

PGM5 (HGNC:):

PGM5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 9-68378303-C-T is Benign according to our data. Variant chr9-68378303-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 770581.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.498 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGM5	NM_021965.4 linkuse as main transcript	c.366C>T	p.Ser122Ser	synonymous_variant	2/11	ENST00000396396.6	NP_068800.2	Q15124-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PGM5	ENST00000396396.6 linkuse as main transcript	c.366C>T	p.Ser122Ser	synonymous_variant	2/11	2	NM_021965.4	ENSP00000379678.1	Q15124-1
PGM5	ENST00000396392.5 linkuse as main transcript	c.366C>T	p.Ser122Ser	synonymous_variant	2/8	1		ENSP00000379674.1	Q15124-2
PGM5	ENST00000431583.1 linkuse as main transcript	c.264C>T	p.Ser88Ser	synonymous_variant	2/4	5		ENSP00000394864.1	Q5JTY7
PGM5	ENST00000604870.6 linkuse as main transcript	n.721C>T		non_coding_transcript_exon_variant	5/12	5

Frequencies

GnomAD3 genomes

AF:

0.0462

AC:

6988

AN:

151206

Hom.:

174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0573

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0384

Gnomad ASJ

AF:

0.0332

Gnomad EAS

AF:

0.00752

Gnomad SAS

AF:

0.0115

Gnomad FIN

AF:

0.0467

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0476

Gnomad OTH

AF:

0.0451

GnomAD3 exomes

AF:

0.0333

AC:

7626

AN:

229238

Hom.:

128

AF XY:

0.0335

AC XY:

4164

AN XY:

124342

show subpopulations

Gnomad AFR exome

AF:

0.0553

Gnomad AMR exome

AF:

0.0181

Gnomad ASJ exome

AF:

0.0277

Gnomad EAS exome

AF:

0.00640

Gnomad SAS exome

AF:

0.0163

Gnomad FIN exome

AF:

0.0424

Gnomad NFE exome

AF:

0.0421

Gnomad OTH exome

AF:

0.0340

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0408

AC:

58529

AN:

1435118

Hom.:

1246

Cov.:

AF XY:

0.0402

AC XY:

28654

AN XY:

713264

show subpopulations

Gnomad4 AFR exome

AF:

0.0517

Gnomad4 AMR exome

AF:

0.0190

Gnomad4 ASJ exome

AF:

0.0329

Gnomad4 EAS exome

AF:

0.0153

Gnomad4 SAS exome

AF:

0.0177

Gnomad4 FIN exome

AF:

0.0418

Gnomad4 NFE exome

AF:

0.0441

Gnomad4 OTH exome

AF:

0.0408

GnomAD4 genome

AF:

0.0463

AC:

7003

AN:

151324

Hom.:

175

Cov.:

AF XY:

0.0440

AC XY:

3253

AN XY:

73906

show subpopulations

Gnomad4 AFR

AF:

0.0576

Gnomad4 AMR

AF:

0.0384

Gnomad4 ASJ

AF:

0.0332

Gnomad4 EAS

AF:

0.00754

Gnomad4 SAS

AF:

0.0115

Gnomad4 FIN

AF:

0.0467

Gnomad4 NFE

AF:

0.0476

Gnomad4 OTH

AF:

0.0446

Alfa

AF:

0.0422

Hom.:

Bravo

AF:

0.0487

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.9

DANN

Benign

0.69

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