rs2303012

Variant names:

• chr5-180336923-T-C
• rs2303012
• NM_005110.4:c.116-346A>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.116-346A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,338 control chromosomes in the GnomAD database, including 1,902 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 0.15 (1902 hom., cov: 33)
• Consequence: GFPT2 NM_005110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GFPT2	NM_005110.4	c.116-346A>G		intron_variant	Intron 2 of 18	ENST00000253778.13	NP_005101.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GFPT2	ENST00000253778.13	c.116-346A>G		intron_variant	Intron 2 of 18	1	NM_005110.4	ENSP00000253778.8
GFPT2	ENST00000503546.1	n.235-346A>G		intron_variant	Intron 2 of 2	2
GFPT2	ENST00000518158.5	n.235-346A>G		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23047 AN: 152220 Hom.: 1900 Cov.: 33

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.151 AC: 23057 AN: 152338 Hom.: 1902 Cov.: 33 AF XY: 0.149 AC XY: 11093 AN XY: 74490

African (AFR) AF: 0.0978 AC: 4067 AN: 41592

American (AMR) AF: 0.116 AC: 1783 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3472

East Asian (EAS) AF: 0.188 AC: 971 AN: 5176

South Asian (SAS) AF: 0.128 AC: 619 AN: 4830

European-Finnish (FIN) AF: 0.162 AC: 1723 AN: 10620

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12454 AN: 68020

Other (OTH) AF: 0.148 AC: 314 AN: 2116

Alfa AF: 0.157 Hom.: 621

Bravo AF: 0.144

Asia WGS AF: 0.161 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.25
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2303012; hg19: chr5-179763923;