11-74336638-A-G

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.*14T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 1,554,914 control chromosomes in the GnomAD database, including 314,362 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.58 (26527 hom., cov: 31)
  • Exomes 𝑓: 0.64 (287835 hom.)
• Consequence: PGM2L1 NM_173582.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.620

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=-0.93).
• BP6: Variant 11-74336638-A-G is Benign according to our data. Variant chr11-74336638-A-G is described in ClinVar as [Benign]. Clinvar id is 1285855.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2L1	NM_173582.6	c.*14T>C		3_prime_UTR_variant	14/14	ENST00000298198.5
LOC112268078	XR_002957258.2	n.314+7150A>G		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.*14T>C		3_prime_UTR_variant	15/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.*14T>C		3_prime_UTR_variant	14/14	1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87935 AN: 151888 Hom.: 26515 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.572

GnomAD3 exomes AF: 0.643 AC: 153645 AN: 238998 Hom.: 50471 AF XY: 0.642 AC XY: 83010 AN XY: 129224

Gnomad AFR exome AF: 0.401

Gnomad AMR exome AF: 0.682

Gnomad ASJ exome AF: 0.605

Gnomad EAS exome AF: 0.810

Gnomad SAS exome AF: 0.640

Gnomad FIN exome AF: 0.717

Gnomad NFE exome AF: 0.630

Gnomad OTH exome AF: 0.632

GnomAD4 exome AF: 0.638 AC: 894791 AN: 1402906 Hom.: 287835 Cov.: 24 AF XY: 0.638 AC XY: 446713 AN XY: 700274

Gnomad4 AFR exome AF: 0.387

Gnomad4 AMR exome AF: 0.678

Gnomad4 ASJ exome AF: 0.606

Gnomad4 EAS exome AF: 0.754

Gnomad4 SAS exome AF: 0.641

Gnomad4 FIN exome AF: 0.713

Gnomad4 NFE exome AF: 0.637

Gnomad4 OTH exome AF: 0.631

GnomAD4 genome AF: 0.579 AC: 87989 AN: 152008 Hom.: 26527 Cov.: 31 AF XY: 0.587 AC XY: 43624 AN XY: 74312

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.572

Alfa AF: 0.616 Hom.: 29799

Bravo AF: 0.565

Asia WGS AF: 0.691 AC: 2405 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	-0.93
Cadd	Benign	0.61
Dann	Benign	0.20

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: rs1044782; hg19: chr11-74047683; COSMIC: COSV53346755;