Variant 2-69338431-TAA-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001244710.2(GFPT1):c.1324+13delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,606,626 control chromosomes in the GnomAD database, including 18,915 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1400 hom., cov: 30)

Exomes 𝑓: 0.15 ( 17515 hom. )

Consequence

GFPT1
NM_001244710.2 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.763

Variant links:

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]

GFPT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 2-69338431-TA-T is Benign according to our data. Variant chr2-69338431-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 257667.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-69338431-TA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
GFPT1	NM_001244710.2 linkuse as main transcript	c.1324+13delT	intron_variant	ENST00000357308.9	NP_001231639.1	Q06210-1
GFPT1	NM_002056.4 linkuse as main transcript	c.1270+13delT	intron_variant		NP_002047.2	Q06210-2
GFPT1	XM_017003801.2 linkuse as main transcript	c.1399+13delT	intron_variant		XP_016859290.1
GFPT1	XM_017003802.3 linkuse as main transcript	c.1345+13delT	intron_variant		XP_016859291.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
GFPT1	ENST00000357308.9 linkuse as main transcript	c.1324+13delT	intron_variant	5	NM_001244710.2	ENSP00000349860.4	Q06210-1
GFPT1	ENST00000361060.5 linkuse as main transcript	c.1270+13delT	intron_variant	1		ENSP00000354347.4	Q06210-2
GFPT1	ENST00000674507.1 linkuse as main transcript	c.1270+13delT	intron_variant			ENSP00000501332.1	A0A6I8PTT9
GFPT1	ENST00000674438.1 linkuse as main transcript	c.1054+13delT	intron_variant			ENSP00000501469.1	A0A6I8PRN4

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19434

AN:

152104

Hom.:

1400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0953

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.0997

Gnomad ASJ

AF:

0.0969

Gnomad EAS

AF:

0.0379

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.123

AC:

30767

AN:

250048

Hom.:

2155

AF XY:

0.127

AC XY:

17218

AN XY:

135124

show subpopulations

Gnomad AFR exome

AF:

0.0931

Gnomad AMR exome

AF:

0.0676

Gnomad ASJ exome

AF:

0.102

Gnomad EAS exome

AF:

0.0300

Gnomad SAS exome

AF:

0.132

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.150

AC:

218191

AN:

1454404

Hom.:

17515

Cov.:

AF XY:

0.150

AC XY:

108737

AN XY:

723904

show subpopulations

Gnomad4 AFR exome

AF:

0.0945

Gnomad4 AMR exome

AF:

0.0708

Gnomad4 ASJ exome

AF:

0.0987

Gnomad4 EAS exome

AF:

0.0183

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.137

Gnomad4 NFE exome

AF:

0.164

Gnomad4 OTH exome

AF:

0.139

GnomAD4 genome

AF:

0.128

AC:

19438

AN:

152222

Hom.:

1400

Cov.:

AF XY:

0.125

AC XY:

9294

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0952

Gnomad4 AMR

AF:

0.0995

Gnomad4 ASJ

AF:

0.0969

Gnomad4 EAS

AF:

0.0378

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.160

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.138

Hom.:

272

Bravo

AF:

0.122

Asia WGS

AF:

0.0890

AC:

310

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital Myasthenic Syndrome, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 29, 2018

- -

Congenital myasthenic syndrome 12

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over