Variant 9-68378237-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_021965.4(PGM5):c.300G>A(p.Ser100Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00555 in 1,561,640 control chromosomes in the GnomAD database, including 396 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 210 hom., cov: 27)

Exomes 𝑓: 0.0031 ( 186 hom. )

Consequence

PGM5
NM_021965.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.520

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 9-68378237-G-A is Benign according to our data. Variant chr9-68378237-G-A is described in ClinVar as [Benign]. Clinvar id is 778427.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.52 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 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.300G>A	p.Ser100Ser	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.300G>A	p.Ser100Ser	synonymous_variant	2/11	2	NM_021965.4	ENSP00000379678.1	Q15124-1
PGM5	ENST00000396392.5 linkuse as main transcript	c.300G>A	p.Ser100Ser	synonymous_variant	2/8	1		ENSP00000379674.1	Q15124-2
PGM5	ENST00000431583.1 linkuse as main transcript	c.198G>A	p.Ser66Ser	synonymous_variant	2/4	5		ENSP00000394864.1	Q5JTY7
PGM5	ENST00000604870.6 linkuse as main transcript	n.655G>A		non_coding_transcript_exon_variant	5/12	5

Frequencies

GnomAD3 genomes

AF:

0.0305

AC:

4319

AN:

141708

Hom.:

211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0178

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000207

Gnomad SAS

AF:

0.000450

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00658

Gnomad NFE

AF:

0.000340

Gnomad OTH

AF:

0.0180

GnomAD3 exomes

AF:

0.00822

AC:

1765

AN:

214618

Hom.:

AF XY:

0.00621

AC XY:

722

AN XY:

116332

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.00730

Gnomad ASJ exome

AF:

0.000412

Gnomad EAS exome

AF:

0.000120

Gnomad SAS exome

AF:

0.000253

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000378

Gnomad OTH exome

AF:

0.00400

GnomAD4 exome

AF:

0.00306

AC:

4343

AN:

1419834

Hom.:

186

Cov.:

AF XY:

0.00264

AC XY:

1864

AN XY:

705294

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.00744

Gnomad4 ASJ exome

AF:

0.0000827

Gnomad4 EAS exome

AF:

0.0000515

Gnomad4 SAS exome

AF:

0.000294

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000414

Gnomad4 OTH exome

AF:

0.00738

GnomAD4 genome

AF:

0.0305

AC:

4331

AN:

141806

Hom.:

210

Cov.:

AF XY:

0.0301

AC XY:

2074

AN XY:

68810

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0178

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000207

Gnomad4 SAS

AF:

0.000450

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000340

Gnomad4 OTH

AF:

0.0178

Alfa

AF:

0.0159

Hom.:

Bravo

AF:

0.0345

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 04, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

0.17

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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