5-180300957-C-T

Position:

• chr5-180300957-C-T

Variant summary

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

The NM_005110.4(GFPT2):​c.*607G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,656 control chromosomes in the GnomAD database, including 2,453 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 0.17 (2452 hom., cov: 33)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: GFPT2 NM_005110.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFPT2	NM_005110.4	c.*607G>A		3_prime_UTR_variant	19/19	ENST00000253778.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFPT2	ENST00000253778.13	c.*607G>A		3_prime_UTR_variant	19/19	1	NM_005110.4	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26178 AN: 151986 Hom.: 2452 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.127 AC: 70 AN: 550 Hom.: 1 Cov.: 0 AF XY: 0.132 AC XY: 44 AN XY: 334

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.124

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.172 AC: 26183 AN: 152106 Hom.: 2452 Cov.: 33 AF XY: 0.171 AC XY: 12728 AN XY: 74346

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.198

Alfa AF: 0.186 Hom.: 4585

Bravo AF: 0.176

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.68

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: rs7725; hg19: chr5-179727957;