11-74336824-A-AT

Position:

• chr11-74336824-A-AT

Variant summary

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

The NM_173582.6(PGM2L1):​c.1767-71_1767-70insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00559 in 1,056,198 control chromosomes in the GnomAD database, including 252 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.025 (163 hom., cov: 32)
  • Exomes 𝑓: 0.0023 (89 hom.)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.03

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 11-74336824-A-AT is Benign according to our data. Variant chr11-74336824-A-AT is described in ClinVar as [Benign]. Clinvar id is 1232198.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGM2L1	NM_173582.6	c.1767-71_1767-70insA		intron_variant		ENST00000298198.5
LOC112268078	XR_002957258.2	n.314+7342dup		intron_variant, non_coding_transcript_variant
PGM2L1	XM_011544953.4	c.1830-71_1830-70insA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGM2L1	ENST00000298198.5	c.1767-71_1767-70insA		intron_variant		1	NM_173582.6	P1

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3861 AN: 152102 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0890

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00812

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

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: 0.00225 AC: 2035 AN: 903978 Hom.: 89 AF XY: 0.00204 AC XY: 940 AN XY: 461388

Gnomad4 AFR exome AF: 0.0829

Gnomad4 AMR exome AF: 0.00473

Gnomad4 ASJ exome AF: 0.0000556

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000128

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000943

Gnomad4 OTH exome AF: 0.00565

GnomAD4 genome AF: 0.0254 AC: 3873 AN: 152220 Hom.: 163 Cov.: 32 AF XY: 0.0242 AC XY: 1798 AN XY: 74438

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.00811

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0196 Hom.: 9

Bravo AF: 0.0288

Asia WGS AF: 0.00433 AC: 16 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

- -

Computational scores

Source: dbNSFP v4.3

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: rs139050358; hg19: chr11-74047869;