9-94603438-T-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000507.4(FBP1):c.960A>G(p.Gly320Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 1,613,744 control chromosomes in the GnomAD database, including 586,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.89 ( 59897 hom., cov: 29)

Exomes 𝑓: 0.85 ( 526322 hom. )

Consequence

FBP1
NM_000507.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.565

Variant links:

Genes affected

FBP1 (HGNC:3606): (fructose-bisphosphatase 1) Fructose-1,6-bisphosphatase 1, a gluconeogenesis regulatory enzyme, catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. Fructose-1,6-diphosphatase deficiency is associated with hypoglycemia and metabolic acidosis. [provided by RefSeq, Jul 2008]

FBP1 links:

PCAT7 (HGNC:48824): (prostate cancer associated transcript 7)

PCAT7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 9-94603438-T-C is Benign according to our data. Variant chr9-94603438-T-C is described in ClinVar as [Benign]. Clinvar id is 256326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-94603438-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.565 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBP1	NM_000507.4 link	c.960A>G	p.Gly320Gly	synonymous_variant	Exon 7 of 7	ENST00000375326.9	NP_000498.2	P09467
FBP1	NM_001127628.2 link	c.960A>G	p.Gly320Gly	synonymous_variant	Exon 8 of 8		NP_001121100.1	P09467Q2TU34
FBP1	XM_006717005.5 link	c.714A>G	p.Gly238Gly	synonymous_variant	Exon 7 of 7		XP_006717068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBP1	ENST00000375326.9 link	c.960A>G	p.Gly320Gly	synonymous_variant	Exon 7 of 7	1	NM_000507.4	ENSP00000364475.5		P09467

Frequencies

GnomAD3 genomes

AF:

0.885

AC:

134553

AN:

151982

Hom.:

59837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.967

Gnomad AMI

AF:

0.915

Gnomad AMR

AF:

0.886

Gnomad ASJ

AF:

0.900

Gnomad EAS

AF:

0.959

Gnomad SAS

AF:

0.812

Gnomad FIN

AF:

0.795

Gnomad MID

AF:

0.833

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.876

GnomAD3 exomes

AF:

0.863

AC:

216541

AN:

251062

Hom.:

93657

AF XY:

0.857

AC XY:

116210

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.968

Gnomad AMR exome

AF:

0.898

Gnomad ASJ exome

AF:

0.886

Gnomad EAS exome

AF:

0.956

Gnomad SAS exome

AF:

0.804

Gnomad FIN exome

AF:

0.806

Gnomad NFE exome

AF:

0.846

Gnomad OTH exome

AF:

0.854

GnomAD4 exome

AF:

0.848

AC:

1239378

AN:

1461644

Hom.:

526322

Cov.:

AF XY:

0.846

AC XY:

615367

AN XY:

727102

show subpopulations

Gnomad4 AFR exome

AF:

0.967

Gnomad4 AMR exome

AF:

0.899

Gnomad4 ASJ exome

AF:

0.885

Gnomad4 EAS exome

AF:

0.953

Gnomad4 SAS exome

AF:

0.803

Gnomad4 FIN exome

AF:

0.814

Gnomad4 NFE exome

AF:

0.842

Gnomad4 OTH exome

AF:

0.861

GnomAD4 genome

AF:

0.885

AC:

134673

AN:

152100

Hom.:

59897

Cov.:

AF XY:

0.880

AC XY:

65418

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.967

Gnomad4 AMR

AF:

0.886

Gnomad4 ASJ

AF:

0.900

Gnomad4 EAS

AF:

0.959

Gnomad4 SAS

AF:

0.811

Gnomad4 FIN

AF:

0.795

Gnomad4 NFE

AF:

0.848

Gnomad4 OTH

AF:

0.878

Alfa

AF:

0.864

Hom.:

24162

Bravo

AF:

0.896

Asia WGS

AF:

0.873

AC:

3034

AN:

3478

EpiCase

AF:

0.847

EpiControl

AF:

0.842

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Fructose-biphosphatase deficiency

Benign:4

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Jul 07, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:3

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

6.1

DANN

Benign

0.50

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