5-180336290-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005110.4(GFPT2):​c.214+189C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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>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.214+189C>G		intron	N/A	ENSP00000253778.8	O94808
	GFPT2	ENST00000889627.1		c.214+189C>G		intron	N/A	ENSP00000559686.1
	GFPT2	ENST00000920229.1		c.214+189C>G		intron	N/A	ENSP00000590288.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 468192 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 248568

African (AFR) AF: 0.00 AC: 0 AN: 12814

American (AMR) AF: 0.00 AC: 0 AN: 19750

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13942

East Asian (EAS) AF: 0.00 AC: 0 AN: 32288

South Asian (SAS) AF: 0.00 AC: 0 AN: 47312

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33512

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2012

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 279870

Other (OTH) AF: 0.00 AC: 0 AN: 26692

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.42
PhyloP100		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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;