5-180304014-T-C

Position:

• chr5-180304014-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005110.4(GFPT2):​c.1842+758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,842 control chromosomes in the GnomAD database, including 25,289 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 0.57 (25289 hom., cov: 30)
• Consequence: GFPT2 NM_005110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

GFPT2 (HGNC:4242): (glutamine-fructose-6-phosphate transaminase 2) Predicted to enable glutamine-fructose-6-phosphate transaminase (isomerizing) activity. Predicted to be involved in UDP-N-acetylglucosamine metabolic process; fructose 6-phosphate metabolic process; and protein N-linked glycosylation. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in cytosol. Implicated in type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFPT2	NM_005110.4	c.1842+758A>G		intron_variant		ENST00000253778.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFPT2	ENST00000253778.13	c.1842+758A>G		intron_variant		1	NM_005110.4	P1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86396 AN: 151726 Hom.: 25277 Cov.: 30

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.569 AC: 86443 AN: 151842 Hom.: 25289 Cov.: 30 AF XY: 0.570 AC XY: 42311 AN XY: 74188

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.592

Alfa AF: 0.616 Hom.: 22360

Bravo AF: 0.569

Asia WGS AF: 0.660 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.40

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: rs6879260; hg19: chr5-179731014;