11-74339128-A-G

Variant names:

• chr11-74339128-A-G
• rs1279293
• NM_173582.6:c.1633-527T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173582.6(PGM2L1):​c.1633-527T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,960 control chromosomes in the GnomAD database, including 39,926 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (39926 hom., cov: 30)
• Consequence: PGM2L1 NM_173582.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

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]

PGM2L1 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ENSG00000308977 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PGM2L1	NM_173582.6	c.1633-527T>C		intron_variant	Intron 12 of 13	ENST00000298198.5	NP_775853.2
PGM2L1	XM_011544953.4	c.1696-527T>C		intron_variant	Intron 13 of 14		XP_011543255.1
LOC112268078	XR_002957258.2	n.314+9640A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGM2L1	ENST00000298198.5	c.1633-527T>C		intron_variant	Intron 12 of 13	1	NM_173582.6	ENSP00000298198.4
ENSG00000308977	ENST00000837614.1	n.518+9640A>G		intron_variant	Intron 2 of 2
ENSG00000308977	ENST00000837615.1	n.194-6456A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109129 AN: 151842 Hom.: 39877 Cov.: 30

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.753

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.719 AC: 109239 AN: 151960 Hom.: 39926 Cov.: 30 AF XY: 0.711 AC XY: 52792 AN XY: 74258

African (AFR) AF: 0.844 AC: 35003 AN: 41450

American (AMR) AF: 0.706 AC: 10773 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2558 AN: 3464

East Asian (EAS) AF: 0.617 AC: 3185 AN: 5164

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4816

European-Finnish (FIN) AF: 0.533 AC: 5620 AN: 10536

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46292 AN: 67946

Other (OTH) AF: 0.756 AC: 1600 AN: 2116

Alfa AF: 0.697 Hom.: 65609

Bravo AF: 0.739

Asia WGS AF: 0.666 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.21
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1279293; hg19: chr11-74050173;