Variant 9-94605616-TAAGA-T 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_000507.4(FBP1):c.706-44_706-41del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 1,607,244 control chromosomes in the GnomAD database, including 6,310 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 655 hom., cov: 31)

Exomes 𝑓: 0.081 ( 5655 hom. )

Consequence

FBP1
NM_000507.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.150

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-94605616-TAAGA-T is Benign according to our data. Variant chr9-94605616-TAAGA-T is described in ClinVar as [Benign]. Clinvar id is 256325.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
FBP1	NM_000507.4 linkuse as main transcript	c.706-44_706-41del	intron_variant	ENST00000375326.9
FBP1	NM_001127628.2 linkuse as main transcript	c.706-44_706-41del	intron_variant
FBP1	XM_006717005.5 linkuse as main transcript	c.460-44_460-41del	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
FBP1	ENST00000375326.9 linkuse as main transcript	c.706-44_706-41del	intron_variant	1	NM_000507.4	P1
FBP1	ENST00000415431.5 linkuse as main transcript	c.706-44_706-41del	intron_variant	2		P1
FBP1	ENST00000648117.1 linkuse as main transcript	c.511-44_511-41del	intron_variant
FBP1	ENST00000682520.1 linkuse as main transcript	c.143-44_143-41del	intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0851

AC:

12932

AN:

151994

Hom.:

651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0820

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.0411

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0687

Gnomad OTH

AF:

0.0868

GnomAD3 exomes

AF:

0.102

AC:

24551

AN:

241162

Hom.:

1617

AF XY:

0.100

AC XY:

13062

AN XY:

130644

show subpopulations

Gnomad AFR exome

AF:

0.0810

Gnomad AMR exome

AF:

0.183

Gnomad ASJ exome

AF:

0.104

Gnomad EAS exome

AF:

0.222

Gnomad SAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.0444

Gnomad NFE exome

AF:

0.0649

Gnomad OTH exome

AF:

0.0876

GnomAD4 exome

AF:

0.0806

AC:

117276

AN:

1455132

Hom.:

5655

AF XY:

0.0816

AC XY:

59041

AN XY:

723726

show subpopulations

Gnomad4 AFR exome

AF:

0.0807

Gnomad4 AMR exome

AF:

0.178

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.0442

Gnomad4 NFE exome

AF:

0.0701

Gnomad4 OTH exome

AF:

0.0964

GnomAD4 genome

AF:

0.0851

AC:

12952

AN:

152112

Hom.:

655

Cov.:

AF XY:

0.0858

AC XY:

6376

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0819

Gnomad4 AMR

AF:

0.138

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.217

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.0411

Gnomad4 NFE

AF:

0.0686

Gnomad4 OTH

AF:

0.0911

Alfa

AF:

0.0784

Hom.:

Bravo

AF:

0.0942

Asia WGS

AF:

0.179

AC:

621

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

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