rs113734896

chr2-69338431-TAA-Tchr2-69338431-TAA-TAchr2-69338431-TAA-TAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001244710.2(GFPT1):c.1324+12_1324+13del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: GFPT1 NM_001244710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

Genes affected

GFPT1 (HGNC:4241): (glutamine--fructose-6-phosphate transaminase 1) This gene encodes the first and rate-limiting enzyme of the hexosamine pathway and controls the flux of glucose into the hexosamine pathway. The product of this gene catalyzes the formation of glucosamine 6-phosphate. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFPT1	NM_001244710.2	c.1324+12_1324+13del		intron_variant		ENST00000357308.9
GFPT1	NM_002056.4	c.1270+12_1270+13del		intron_variant
GFPT1	XM_017003801.2	c.1399+12_1399+13del		intron_variant
GFPT1	XM_017003802.3	c.1345+12_1345+13del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFPT1	ENST00000357308.9	c.1324+12_1324+13del		intron_variant		5	NM_001244710.2
GFPT1	ENST00000361060.5	c.1270+12_1270+13del		intron_variant		1		P1
GFPT1	ENST00000674438.1	c.1054+12_1054+13del		intron_variant
GFPT1	ENST00000674507.1	c.1270+12_1270+13del		intron_variant

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs113734896; hg19: chr2-69565563;