dbSNP rs9695: FBP1:c.*21C>T (chr9-94603360-G-A) – ACMG Classification: Benign (-20 pts)

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.*21C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,603,824 control chromosomes in the GnomAD database, including 206,469 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 20119 hom., cov: 32)

Exomes 𝑓: 0.50 ( 186350 hom. )

Consequence

FBP1
NM_000507.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.05

Publications

17 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 links:

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

PCAT7 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=-0.81).

BP6

Variant 9-94603360-G-A is Benign according to our data. Variant chr9-94603360-G-A is described in ClinVar as Benign. ClinVar VariationId is 256318.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000507.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP1	NM_000507.4	MANE Select	c.*21C>T		3_prime_UTR	Exon 7 of 7	NP_000498.2
	FBP1	NM_001127628.2		c.*21C>T		3_prime_UTR	Exon 8 of 8	NP_001121100.1	P09467

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FBP1	ENST00000375326.9	TSL:1 MANE Select	c.*21C>T	3_prime_UTR	Exon 7 of 7	ENSP00000364475.5	P09467
FBP1	ENST00000884868.1		c.*21C>T	3_prime_UTR	Exon 8 of 8	ENSP00000554927.1
FBP1	ENST00000945615.1		c.*21C>T	3_prime_UTR	Exon 7 of 7	ENSP00000615674.1

Frequencies

GnomAD3 genomes

AF:

0.512

AC:

77802

AN:

151822

Hom.:

20105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.490

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.680

Gnomad EAS

AF:

0.413

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.515

Gnomad OTH

AF:

0.541

GnomAD2 exomes

AF:

0.515

AC:

125573

AN:

243660

AF XY:

0.509

show subpopulations

Gnomad AFR exome

AF:

0.486

Gnomad AMR exome

AF:

0.697

Gnomad ASJ exome

AF:

0.658

Gnomad EAS exome

AF:

0.398

Gnomad FIN exome

AF:

0.426

Gnomad NFE exome

AF:

0.510

Gnomad OTH exome

AF:

0.526

GnomAD4 exome

AF:

0.503

AC:

730395

AN:

1451884

Hom.:

186350

Cov.:

AF XY:

0.501

AC XY:

362128

AN XY:

722176

show subpopulations

African (AFR)

AF:

0.495

AC:

16467

AN:

33270

American (AMR)

AF:

0.695

AC:

30661

AN:

44102

Ashkenazi Jewish (ASJ)

AF:

0.658

AC:

17099

AN:

25994

East Asian (EAS)

AF:

0.391

AC:

15428

AN:

39476

South Asian (SAS)

AF:

0.435

AC:

37144

AN:

85370

European-Finnish (FIN)

AF:

0.425

AC:

22621

AN:

53172

Middle Eastern (MID)

AF:

0.539

AC:

3004

AN:

5572

European-Non Finnish (NFE)

AF:

0.504

AC:

556662

AN:

1104912

Other (OTH)

AF:

0.522

AC:

31309

AN:

60016

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

16939

33879

50818

67758

84697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16080

32160

48240

64320

80400

<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:

0.512

AC:

77858

AN:

151940

Hom.:

20119

Cov.:

AF XY:

0.509

AC XY:

37766

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.490

AC:

20287

AN:

41442

American (AMR)

AF:

0.634

AC:

9674

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.680

AC:

2357

AN:

3464

East Asian (EAS)

AF:

0.413

AC:

2125

AN:

5146

South Asian (SAS)

AF:

0.432

AC:

2077

AN:

4804

European-Finnish (FIN)

AF:

0.418

AC:

4411

AN:

10558

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.515

AC:

35020

AN:

67960

Other (OTH)

AF:

0.540

AC:

1135

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1964

3928

5892

7856

9820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.523

Hom.:

60273

Bravo

AF:

0.529

Asia WGS

AF:

0.433

AC:

1506

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Fructose-biphosphatase deficiency (2)

not provided (2)

not specified (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.3

(source)

DANN

Benign

0.67

PhyloP100

-1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over