chr5-180335405-T-C

Position:

• chr5-180335405-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.340+423A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,166 control chromosomes in the GnomAD database, including 1,871 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 (1871 hom., cov: 33)
• Consequence: GFPT2 NM_005110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFPT2	NM_005110.4	c.340+423A>G		intron_variant		ENST00000253778.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFPT2	ENST00000253778.13	c.340+423A>G		intron_variant		1	NM_005110.4	P1
GFPT2	ENST00000518158.5	n.459+423A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22733 AN: 152048 Hom.: 1869 Cov.: 33

Gnomad AFR AF: 0.0916

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.149 AC: 22743 AN: 152166 Hom.: 1871 Cov.: 33 AF XY: 0.147 AC XY: 10922 AN XY: 74396

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.148

Alfa AF: 0.172 Hom.: 1090

Bravo AF: 0.142

Asia WGS AF: 0.160 AC: 555 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	0.12
DANN	Benign	0.47

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: rs17080196; hg19: chr5-179762405;