Variant rs67760762 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001244710.2(GFPT1):c.408+30T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 1,216,722 control chromosomes in the GnomAD database, including 93,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 9054 hom., cov: 32)

Exomes 𝑓: 0.39 ( 84467 hom. )

Consequence

GFPT1
NM_001244710.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.553

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 2-69359238-A-G is Benign according to our data. Variant chr2-69359238-A-G is described in ClinVar as [Benign]. Clinvar id is 258543.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-69359238-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
GFPT1	NM_001244710.2 linkuse as main transcript	c.408+30T>C	intron_variant	ENST00000357308.9	NP_001231639.1	Q06210-1
GFPT1	NM_002056.4 linkuse as main transcript	c.408+30T>C	intron_variant		NP_002047.2	Q06210-2
GFPT1	XM_017003801.2 linkuse as main transcript	c.483+30T>C	intron_variant		XP_016859290.1
GFPT1	XM_017003802.3 linkuse as main transcript	c.483+30T>C	intron_variant		XP_016859291.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
GFPT1	ENST00000357308.9 linkuse as main transcript	c.408+30T>C	intron_variant	5	NM_001244710.2	ENSP00000349860.4	Q06210-1
GFPT1	ENST00000361060.5 linkuse as main transcript	c.408+30T>C	intron_variant	1		ENSP00000354347.4	Q06210-2
GFPT1	ENST00000674507.1 linkuse as main transcript	c.408+30T>C	intron_variant			ENSP00000501332.1	A0A6I8PTT9
GFPT1	ENST00000674438.1 linkuse as main transcript	c.192+30T>C	intron_variant			ENSP00000501469.1	A0A6I8PRN4

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47295

AN:

151960

Hom.:

9042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0850

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.352

GnomAD3 exomes

AF:

0.370

AC:

92875

AN:

250888

Hom.:

18674

AF XY:

0.375

AC XY:

50851

AN XY:

135608

show subpopulations

Gnomad AFR exome

AF:

0.0745

Gnomad AMR exome

AF:

0.385

Gnomad ASJ exome

AF:

0.551

Gnomad EAS exome

AF:

0.215

Gnomad SAS exome

AF:

0.328

Gnomad FIN exome

AF:

0.383

Gnomad NFE exome

AF:

0.424

Gnomad OTH exome

AF:

0.408

GnomAD4 exome

AF:

0.389

AC:

413765

AN:

1064642

Hom.:

84467

Cov.:

AF XY:

0.389

AC XY:

213123

AN XY:

548196

show subpopulations

Gnomad4 AFR exome

AF:

0.0706

Gnomad4 AMR exome

AF:

0.384

Gnomad4 ASJ exome

AF:

0.549

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.332

Gnomad4 FIN exome

AF:

0.383

Gnomad4 NFE exome

AF:

0.411

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

AF:

0.311

AC:

47313

AN:

152080

Hom.:

9054

Cov.:

AF XY:

0.311

AC XY:

23121

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.0848

Gnomad4 AMR

AF:

0.372

Gnomad4 ASJ

AF:

0.531

Gnomad4 EAS

AF:

0.200

Gnomad4 SAS

AF:

0.338

Gnomad4 FIN

AF:

0.374

Gnomad4 NFE

AF:

0.417

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.326

Hom.:

1609

Bravo

AF:

0.301

Asia WGS

AF:

0.288

AC:

1001

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital myasthenic syndrome 12

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.2

DANN

Benign

0.67

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

2.0

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