rs2297084

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000507.4(FBP1):c.705+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,610,456 control chromosomes in the GnomAD database, including 206,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 19869 hom., cov: 33)

Exomes 𝑓: 0.50 ( 187083 hom. )

Consequence

FBP1
NM_000507.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.879

Publications

11 publications found

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 Gene-Disease associations (from GenCC):

fructose-1,6-bisphosphatase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Genomics England PanelApp, Orphanet

FBP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-94606801-G-A is Benign according to our data. Variant chr9-94606801-G-A is described in ClinVar as Benign. ClinVar VariationId is 256324.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
FBP1	NM_000507.4 link	c.705+14C>T	intron_variant	Intron 5 of 6	ENST00000375326.9	NP_000498.2
FBP1	NM_001127628.2 link	c.705+14C>T	intron_variant	Intron 6 of 7		NP_001121100.1
FBP1	XM_006717005.5 link	c.459+14C>T	intron_variant	Intron 5 of 6		XP_006717068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBP1	ENST00000375326.9 link	c.705+14C>T		intron_variant	Intron 5 of 6	1	NM_000507.4	ENSP00000364475.5

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77319

AN:

151950

Hom.:

19854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.478

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.680

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.537

GnomAD2 exomes

AF:

0.517

AC:

127174

AN:

246200

AF XY:

0.511

show subpopulations

Gnomad AFR exome

AF:

0.475

Gnomad AMR exome

AF:

0.698

Gnomad ASJ exome

AF:

0.659

Gnomad EAS exome

AF:

0.398

Gnomad FIN exome

AF:

0.430

Gnomad NFE exome

AF:

0.514

Gnomad OTH exome

AF:

0.528

GnomAD4 exome

AF:

0.503

AC:

733738

AN:

1458388

Hom.:

187083

Cov.:

AF XY:

0.501

AC XY:

363778

AN XY:

725448

show subpopulations

African (AFR)

AF:

0.483

AC:

16131

AN:

33424

American (AMR)

AF:

0.696

AC:

30808

AN:

44296

Ashkenazi Jewish (ASJ)

AF:

0.658

AC:

17169

AN:

26090

East Asian (EAS)

AF:

0.391

AC:

15477

AN:

39622

South Asian (SAS)

AF:

0.434

AC:

37386

AN:

86088

European-Finnish (FIN)

AF:

0.426

AC:

22708

AN:

53298

Middle Eastern (MID)

AF:

0.545

AC:

2952

AN:

5418

European-Non Finnish (NFE)

AF:

0.504

AC:

559692

AN:

1109916

Other (OTH)

AF:

0.522

AC:

31415

AN:

60236

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

17750

35501

53251

71002

88752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16188

32376

48564

64752

80940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.509

AC:

77376

AN:

152068

Hom.:

19869

Cov.:

AF XY:

0.506

AC XY:

37575

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.478

AC:

19804

AN:

41474

American (AMR)

AF:

0.633

AC:

9679

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.680

AC:

2359

AN:

3470

East Asian (EAS)

AF:

0.410

AC:

2110

AN:

5142

South Asian (SAS)

AF:

0.431

AC:

2076

AN:

4822

European-Finnish (FIN)

AF:

0.419

AC:

4428

AN:

10576

Middle Eastern (MID)

AF:

0.541

AC:

158

AN:

292

European-Non Finnish (NFE)

AF:

0.515

AC:

35016

AN:

67972

Other (OTH)

AF:

0.536

AC:

1134

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1998

3996

5995

7993

9991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.541

Hom.:

4153

Bravo

AF:

0.525

Asia WGS

AF:

0.433

AC:

1506

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Fructose-biphosphatase deficiency

Benign:3

Jan 13, 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. -

Aug 10, 2021

Genome-Nilou Lab

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 provided

Benign:2

Mar 03, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

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

-0.84

CADD

Benign

0.052

(source)

DANN

Benign

0.67

PhyloP100

-0.88

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over