11-74343301-G-T

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.1312+22C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 1,540,430 control chromosomes in the GnomAD database, including 312,498 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.60 (27740 hom., cov: 31)
  • Exomes 𝑓: 0.64 (284758 hom.)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.30

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=-0.84).
• BP6: Variant 11-74343301-G-T is Benign according to our data. Variant chr11-74343301-G-T is described in ClinVar as [Benign]. Clinvar id is 1236874.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.1312+22C>A		intron_variant		ENST00000298198.5
LOC112268078	XR_002957258.2	n.314+13813G>T		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.1375+22C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.1312+22C>A		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90631 AN: 151842 Hom.: 27731 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.585

GnomAD3 exomes AF: 0.641 AC: 124391 AN: 194092 Hom.: 40550 AF XY: 0.640 AC XY: 68746 AN XY: 107498

Gnomad AFR exome AF: 0.454

Gnomad AMR exome AF: 0.679

Gnomad ASJ exome AF: 0.601

Gnomad EAS exome AF: 0.803

Gnomad SAS exome AF: 0.634

Gnomad FIN exome AF: 0.711

Gnomad NFE exome AF: 0.628

Gnomad OTH exome AF: 0.630

GnomAD4 exome AF: 0.638 AC: 886323 AN: 1388468 Hom.: 284758 Cov.: 34 AF XY: 0.638 AC XY: 438905 AN XY: 687940

Gnomad4 AFR exome AF: 0.445

Gnomad4 AMR exome AF: 0.674

Gnomad4 ASJ exome AF: 0.603

Gnomad4 EAS exome AF: 0.751

Gnomad4 SAS exome AF: 0.637

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.637

Gnomad4 OTH exome AF: 0.634

GnomAD4 genome AF: 0.597 AC: 90671 AN: 151962 Hom.: 27740 Cov.: 31 AF XY: 0.604 AC XY: 44832 AN XY: 74262

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.586

Alfa AF: 0.601 Hom.: 5277

Bravo AF: 0.584

Asia WGS AF: 0.692 AC: 2402 AN: 3470

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	-0.84
Cadd	Benign	0.10
Dann	Benign	0.38

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: rs641271; hg19: chr11-74054346; COSMIC: COSV53346763;