11-74343130-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.1313-116T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 1,381,654 control chromosomes in the GnomAD database, including 2,157 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.040 (194 hom., cov: 32)
  • Exomes 𝑓: 0.050 (1963 hom.)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.989

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=-0.86).
• BP6: Variant 11-74343130-A-G is Benign according to our data. Variant chr11-74343130-A-G is described in ClinVar as [Benign]. Clinvar id is 1221198.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2L1	NM_173582.6	c.1313-116T>C		intron_variant		ENST00000298198.5
LOC112268078	XR_002957258.2	n.314+13642A>G		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.1376-116T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.1313-116T>C		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6063 AN: 152124 Hom.: 194 Cov.: 32

Gnomad AFR AF: 0.00847

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.0473

GnomAD4 exome AF: 0.0500 AC: 61434 AN: 1229412 Hom.: 1963 AF XY: 0.0525 AC XY: 31962 AN XY: 609028

Gnomad4 AFR exome AF: 0.00832

Gnomad4 AMR exome AF: 0.0306

Gnomad4 ASJ exome AF: 0.0873

Gnomad4 EAS exome AF: 0.0383

Gnomad4 SAS exome AF: 0.137

Gnomad4 FIN exome AF: 0.0504

Gnomad4 NFE exome AF: 0.0452

Gnomad4 OTH exome AF: 0.0552

GnomAD4 genome AF: 0.0398 AC: 6059 AN: 152242 Hom.: 194 Cov.: 32 AF XY: 0.0418 AC XY: 3114 AN XY: 74444

Gnomad4 AFR AF: 0.00847

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.0399

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0486

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0461 Hom.: 45

Bravo AF: 0.0364

Asia WGS AF: 0.0900 AC: 310 AN: 3476

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 17, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.7
Dann	Benign	0.56

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: rs75415490; hg19: chr11-74054175;