11-74351303-ACACTTTTTAT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_173582.6(PGM2L1):c.749+70_749+79del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00519 in 1,335,786 control chromosomes in the GnomAD database, including 291 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.025 (165 hom., cov: 32)
  • Exomes 𝑓: 0.0026 (126 hom.)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.54

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 -10 ACMG points.

• BP6: Variant 11-74351303-ACACTTTTTAT-A is Benign according to our data. Variant chr11-74351303-ACACTTTTTAT-A is described in ClinVar as [Benign]. Clinvar id is 1268532.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2L1	NM_173582.6	c.749+70_749+79del		intron_variant		ENST00000298198.5
LOC112268078	XR_002957258.2	n.315-16751_315-16742del		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.812+70_812+79del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.749+70_749+79del		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3859 AN: 152194 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00812

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.0158

GnomAD4 exome AF: 0.00259 AC: 3063 AN: 1183474 Hom.: 126 AF XY: 0.00228 AC XY: 1363 AN XY: 597078

Gnomad4 AFR exome AF: 0.0958

Gnomad4 AMR exome AF: 0.00536

Gnomad4 ASJ exome AF: 0.0000446

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000210

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000884

Gnomad4 OTH exome AF: 0.00585

GnomAD4 genome AF: 0.0254 AC: 3871 AN: 152312 Hom.: 165 Cov.: 32 AF XY: 0.0241 AC XY: 1793 AN XY: 74482

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.00811

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.000591 Hom.: 0

Bravo AF: 0.0288

Asia WGS AF: 0.00404 AC: 15 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 26, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149649729; hg19: chr11-74062348;