9-68357096-G-A

Variant names:

• chr9-68357096-G-A
• rs10867824
• NM_021965.4:c.-32G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_021965.4(PGM5):​c.-32G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,444,862 control chromosomes in the GnomAD database, including 116,543 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.39 (11632 hom., cov: 31)
  • Exomes 𝑓: 0.40 (104911 hom.)
• Consequence: PGM5 NM_021965.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -4.36
• Publications: 3 publications found

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-AS1 (HGNC:44181): (PGM5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 9-68357096-G-A is Benign according to our data. Variant chr9-68357096-G-A is described in ClinVar as Benign. ClinVar VariationId is 1278897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021965.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGM5	NM_021965.4	MANE Select	c.-32G>A		5_prime_UTR	Exon 1 of 11	NP_068800.2	Q15124-1
	PGM5-AS1	NR_015423.2		n.144+627C>T		intron	N/A
	PGM5-AS1	NR_121191.1		n.264+507C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGM5	ENST00000396396.6	TSL:2 MANE Select	c.-32G>A		5_prime_UTR	Exon 1 of 11	ENSP00000379678.1	Q15124-1
	PGM5	ENST00000396392.5	TSL:1	c.-32G>A		5_prime_UTR	Exon 1 of 8	ENSP00000379674.1	Q15124-2
	PGM5-AS1	ENST00000417887.1	TSL:1	n.130+627C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58953 AN: 151378 Hom.: 11621 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.412

GnomAD2 exomes AF: 0.417 AC: 27101 AN: 64932 AF XY: 0.415

Gnomad AFR exome AF: 0.384

Gnomad AMR exome AF: 0.500

Gnomad ASJ exome AF: 0.436

Gnomad EAS exome AF: 0.341

Gnomad FIN exome AF: 0.449

Gnomad NFE exome AF: 0.414

Gnomad OTH exome AF: 0.422

GnomAD4 exome AF: 0.401 AC: 519251 AN: 1293376 Hom.: 104911 Cov.: 34 AF XY: 0.400 AC XY: 252209 AN XY: 630290

African (AFR) AF: 0.346 AC: 9304 AN: 26874

American (AMR) AF: 0.484 AC: 11544 AN: 23856

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 8383 AN: 19740

East Asian (EAS) AF: 0.293 AC: 9467 AN: 32266

South Asian (SAS) AF: 0.346 AC: 22803 AN: 65856

European-Finnish (FIN) AF: 0.431 AC: 13453 AN: 31236

Middle Eastern (MID) AF: 0.400 AC: 1480 AN: 3700

European-Non Finnish (NFE) AF: 0.406 AC: 420961 AN: 1036096

Other (OTH) AF: 0.407 AC: 21856 AN: 53752

GnomAD4 genome AF: 0.390 AC: 59007 AN: 151486 Hom.: 11632 Cov.: 31 AF XY: 0.389 AC XY: 28798 AN XY: 73994

African (AFR) AF: 0.337 AC: 13942 AN: 41358

American (AMR) AF: 0.444 AC: 6757 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1516 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1674 AN: 5060

South Asian (SAS) AF: 0.340 AC: 1632 AN: 4804

European-Finnish (FIN) AF: 0.430 AC: 4522 AN: 10522

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.405 AC: 27447 AN: 67748

Other (OTH) AF: 0.418 AC: 879 AN: 2102

Alfa AF: 0.388 Hom.: 1592

Bravo AF: 0.393

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.91
PhyloP100		-4.4
PromoterAI		-0.081	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10867824; hg19: chr9-70972012;