11-74346602-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_173582.6(PGM2L1):c.1037+130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 633,872 control chromosomes in the GnomAD database, including 128,545 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.60 (27739 hom., cov: 32)
  • Exomes 𝑓: 0.64 (100806 hom.)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.285

Genes affected

PGM2L1 (HGNC:20898): (phosphoglucomutase 2 like 1) Enables glucose-1,6-bisphosphate synthase activity. Predicted to be involved in glucose metabolic process and phosphorylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LOC112268078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 11-74346602-T-C is Benign according to our data. Variant chr11-74346602-T-C is described in ClinVar as [Benign]. Clinvar id is 1294901.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2L1	NM_173582.6	c.1037+130A>G		intron_variant		ENST00000298198.5
LOC112268078	XR_002957258.2	n.314+17114T>C		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.1100+130A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.1037+130A>G		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90631 AN: 151944 Hom.: 27731 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.586

GnomAD4 exome AF: 0.643 AC: 309890 AN: 481810 Hom.: 100806 AF XY: 0.642 AC XY: 162359 AN XY: 252898

Gnomad4 AFR exome AF: 0.452

Gnomad4 AMR exome AF: 0.676

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.749

Gnomad4 SAS exome AF: 0.640

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.634

Gnomad4 OTH exome AF: 0.633

GnomAD4 genome AF: 0.596 AC: 90669 AN: 152062 Hom.: 27739 Cov.: 32 AF XY: 0.603 AC XY: 44853 AN XY: 74346

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.586

Alfa AF: 0.613 Hom.: 3610

Bravo AF: 0.584

Asia WGS AF: 0.694 AC: 2413 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.6
Dann	Benign	0.68

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: rs519083; hg19: chr11-74057647; COSMIC: COSV53347319;