Genetic Variant FBP2:c.427-5112G>A (chr9-94576714-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003837.4(FBP2):c.427-5112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,350 control chromosomes in the GnomAD database, including 65,052 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.92 ( 65041 hom., cov: 33)

Exomes 𝑓: 0.88 ( 11 hom. )

Consequence

FBP2
NM_003837.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.94

Variant links:

Genes affected

FBP2 (HGNC:3607): (fructose-bisphosphatase 2) This gene encodes a gluconeogenesis regulatory enzyme which catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. [provided by RefSeq, Jul 2008]

FBP2 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBP2	NM_003837.4 link	c.427-5112G>A		intron_variant	Intron 3 of 6	ENST00000375337.4	NP_003828.2	O00757

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBP2	ENST00000375337.4 link	c.427-5112G>A		intron_variant	Intron 3 of 6	1	NM_003837.4	ENSP00000364486.3		O00757
PCAT7	ENST00000647389.1 link	n.600C>T		non_coding_transcript_exon_variant	Exon 4 of 9

Frequencies

GnomAD3 genomes

AF:

0.924

AC:

140577

AN:

152206

Hom.:

64986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.950

Gnomad AMI

AF:

0.936

Gnomad AMR

AF:

0.895

Gnomad ASJ

AF:

0.943

Gnomad EAS

AF:

0.847

Gnomad SAS

AF:

0.849

Gnomad FIN

AF:

0.935

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.922

Gnomad OTH

AF:

0.932

GnomAD4 exome

AF:

0.885

AC:

AN:

Hom.:

Cov.:

AF XY:

0.850

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.924

AC:

140689

AN:

152324

Hom.:

65041

Cov.:

AF XY:

0.922

AC XY:

68637

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.950

Gnomad4 AMR

AF:

0.895

Gnomad4 ASJ

AF:

0.943

Gnomad4 EAS

AF:

0.847

Gnomad4 SAS

AF:

0.850

Gnomad4 FIN

AF:

0.935

Gnomad4 NFE

AF:

0.922

Gnomad4 OTH

AF:

0.930

Alfa

AF:

0.916

Hom.:

29967

Bravo

AF:

0.920

Asia WGS

AF:

0.859

AC:

2984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

6.3

DANN

Benign

0.62

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over