rs6864729

Variant names:

• chr5-180336290-G-A
• rs6864729
• NM_005110.4:c.214+189C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-180336290-G-A
• chr5-180336290-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005110.4(GFPT2):​c.214+189C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 619,910 control chromosomes in the GnomAD database, including 8,886 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 0.14 (1740 hom., cov: 33)
  • Exomes 𝑓: 0.17 (7146 hom.)
• Consequence: GFPT2 NM_005110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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.214+189C>T		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.214+189C>T		intron	N/A	ENSP00000253778.8	O94808
	GFPT2	ENST00000889627.1		c.214+189C>T		intron	N/A	ENSP00000559686.1
	GFPT2	ENST00000920229.1		c.214+189C>T		intron	N/A	ENSP00000590288.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20760 AN: 151944 Hom.: 1740 Cov.: 33

Gnomad AFR AF: 0.0452

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.171 AC: 79869 AN: 467846 Hom.: 7146 Cov.: 3 AF XY: 0.169 AC XY: 42064 AN XY: 248374

African (AFR) AF: 0.0434 AC: 556 AN: 12814

American (AMR) AF: 0.107 AC: 2113 AN: 19742

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 3356 AN: 13928

East Asian (EAS) AF: 0.194 AC: 6273 AN: 32268

South Asian (SAS) AF: 0.122 AC: 5785 AN: 47274

European-Finnish (FIN) AF: 0.175 AC: 5852 AN: 33482

Middle Eastern (MID) AF: 0.142 AC: 285 AN: 2012

European-Non Finnish (NFE) AF: 0.183 AC: 51213 AN: 279650

Other (OTH) AF: 0.166 AC: 4436 AN: 26676

GnomAD4 genome AF: 0.136 AC: 20754 AN: 152064 Hom.: 1740 Cov.: 33 AF XY: 0.135 AC XY: 10025 AN XY: 74326

African (AFR) AF: 0.0450 AC: 1867 AN: 41516

American (AMR) AF: 0.112 AC: 1714 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.188 AC: 968 AN: 5160

South Asian (SAS) AF: 0.128 AC: 616 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1720 AN: 10548

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12457 AN: 67958

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.144 Hom.: 235

Bravo AF: 0.128

Asia WGS AF: 0.155 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.50
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6864729; hg19: chr5-179763290;