2-69369060-T-C

Position:

• chr2-69369060-T-C

Variant summary

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

The NM_001244710.2(GFPT1):​c.223+941A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,060 control chromosomes in the GnomAD database, including 34,122 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 0.66 (34122 hom., cov: 32)
• Consequence: GFPT1 NM_001244710.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFPT1	NM_001244710.2	c.223+941A>G		intron_variant		ENST00000357308.9
GFPT1	NM_002056.4	c.223+941A>G		intron_variant
GFPT1	XM_017003801.2	c.298+941A>G		intron_variant
GFPT1	XM_017003802.3	c.298+941A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFPT1	ENST00000357308.9	c.223+941A>G		intron_variant		5	NM_001244710.2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99727 AN: 151942 Hom.: 34081 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.656 AC: 99821 AN: 152060 Hom.: 34122 Cov.: 32 AF XY: 0.652 AC XY: 48483 AN XY: 74348

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.632

Alfa AF: 0.560 Hom.: 2382

Bravo AF: 0.663

Asia WGS AF: 0.593 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.74

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: rs13419122; hg19: chr2-69596192;