9-68385385-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_021965.4(PGM5):c.571+841C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.27 (331 hom., cov: 37)
  • Failed GnomAD Quality Control
• Consequence: PGM5 NM_021965.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM5	NM_021965.4	c.571+841C>G		intron_variant		ENST00000396396.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM5	ENST00000396396.6	c.571+841C>G		intron_variant		2	NM_021965.4	P1
PGM5	ENST00000396392.5	c.571+841C>G		intron_variant		1
PGM5	ENST00000431583.1	c.323-2078C>G		intron_variant		5
PGM5	ENST00000604870.6	n.926+841C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 41413 AN: 151240 Hom.: 332 Cov.: 37 FAILED QC

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.274 AC: 41453 AN: 151356 Hom.: 331 Cov.: 37 AF XY: 0.274 AC XY: 20238 AN XY: 73988

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.275

Alfa AF: 0.157 Hom.: 267

Asia WGS AF: 0.260 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs4111290; hg19: chr9-71000301;