Genetic Variant FBP2:p.Ser211Asn (chr9-94567343-C-T) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2

The NM_003837.4(FBP2):c.632G>A(p.Ser211Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 1,614,156 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0051 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 45 hom. )

Consequence

FBP2
NM_003837.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 7.71

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.07704571).

BP6

Variant 9-94567343-C-T is Benign according to our data. Variant chr9-94567343-C-T is described in ClinVar as [Benign]. Clinvar id is 1301656.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00595 (8703/1461844) while in subpopulation MID AF= 0.018 (104/5768). AF 95% confidence interval is 0.0152. There are 45 homozygotes in gnomad4_exome. There are 4393 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 776 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBP2	NM_003837.4 link	c.632G>A	p.Ser211Asn	missense_variant	Exon 5 of 7	ENST00000375337.4	NP_003828.2	O00757

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
FBP2	ENST00000375337.4 link	c.632G>A	p.Ser211Asn	missense_variant	Exon 5 of 7	1	NM_003837.4	ENSP00000364486.3	O00757
PCAT7	ENST00000452148.3 link	n.442-47C>T		intron_variant	Intron 2 of 2	2
PCAT7	ENST00000644721.1 link	n.448-47C>T		intron_variant	Intron 2 of 2
PCAT7	ENST00000647389.1 link	n.442-5636C>T		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.00511

AC:

777

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00615

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00816

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00473

AC:

1189

AN:

251482

Hom.:

AF XY:

0.00528

AC XY:

717

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00344

Gnomad ASJ exome

AF:

0.00496

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00307

Gnomad FIN exome

AF:

0.000970

Gnomad NFE exome

AF:

0.00759

Gnomad OTH exome

AF:

0.00456

GnomAD4 exome

AF:

0.00595

AC:

8703

AN:

1461844

Hom.:

Cov.:

AF XY:

0.00604

AC XY:

4393

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00122

Gnomad4 AMR exome

AF:

0.00414

Gnomad4 ASJ exome

AF:

0.00666

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00322

Gnomad4 FIN exome

AF:

0.00180

Gnomad4 NFE exome

AF:

0.00670

Gnomad4 OTH exome

AF:

0.00624

GnomAD4 genome

AF:

0.00509

AC:

776

AN:

152312

Hom.:

Cov.:

AF XY:

0.00467

AC XY:

348

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00608

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00816

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.00728

Hom.:

Bravo

AF:

0.00487

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00674

AC:

ExAC

AF:

0.00489

AC:

594

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00807

EpiControl

AF:

0.00984

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 06, 2020

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.99

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.12

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.69

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.79

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.94

M_CAP

Uncertain

0.26

MetaRNN

Benign

0.077

MetaSVM

Uncertain

0.46

MutationAssessor

Pathogenic

3.6

PrimateAI

Uncertain

0.65

PROVEAN

Uncertain

-2.9

REVEL

Pathogenic

0.79

Sift

Uncertain

0.012

Sift4G

Uncertain

0.010

Polyphen

0.93

Vest4

0.93

MVP

0.90

MPC

0.54

ClinPred

0.057

GERP RS

5.2

Varity_R

0.86

gMVP

0.90

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