chr5-180304014-T-C

Variant names:

• chr5-180304014-T-C
• rs6879260
• NM_005110.4:c.1842+758A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 49 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005110.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GFPT2	NM_005110.4	MANE Select	c.1842+758A>G		intron	N/A	NP_005101.1	A0A0S2Z4X9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GFPT2	ENST00000253778.13	TSL:1 MANE Select	c.1842+758A>G		intron	N/A	ENSP00000253778.8	O94808
	GFPT2	ENST00000889627.1		c.1905+758A>G		intron	N/A	ENSP00000559686.1
	GFPT2	ENST00000920229.1		c.1839+758A>G		intron	N/A	ENSP00000590288.1

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

African (AFR) AF: 0.431 AC: 17840 AN: 41378

American (AMR) AF: 0.613 AC: 9358 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3470

East Asian (EAS) AF: 0.834 AC: 4294 AN: 5148

South Asian (SAS) AF: 0.569 AC: 2726 AN: 4794

European-Finnish (FIN) AF: 0.587 AC: 6187 AN: 10536

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41679 AN: 67932

Other (OTH) AF: 0.592 AC: 1250 AN: 2112

Alfa AF: 0.603 Hom.: 68908

Bravo AF: 0.569

Asia WGS AF: 0.660 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.40
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: rs6879260; hg19: chr5-179731014;