chr9-94567343-C-T

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

6
9
4

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

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
FBP2NM_003837.4 linkc.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 Appris UniProt
FBP2ENST00000375337.4 linkc.632G>A p.Ser211Asn missense_variant Exon 5 of 7 1 NM_003837.4 ENSP00000364486.3 O00757
PCAT7ENST00000452148.3 linkn.442-47C>T intron_variant Intron 2 of 2 2
PCAT7ENST00000644721.1 linkn.448-47C>T intron_variant Intron 2 of 2
PCAT7ENST00000647389.1 linkn.442-5636C>T intron_variant Intron 2 of 8

Frequencies

GnomAD3 genomes
AF:
0.00511
AC:
777
AN:
152194
Hom.:
4
Cov.:
32
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.:
8
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.:
45
Cov.:
32
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.:
4
Cov.:
32
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.:
5
Bravo
AF:
0.00487
TwinsUK
AF:
0.00378
AC:
14
ALSPAC
AF:
0.00675
AC:
26
ESP6500AA
AF:
0.00136
AC:
6
ESP6500EA
AF:
0.00674
AC:
58
ExAC
AF:
0.00489
AC:
594
Asia WGS
AF:
0.00202
AC:
7
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
Benign, criteria provided, single submitterclinical testingAl Jalila Children’s Genomics Center, Al Jalila Childrens Speciality HospitalJan 06, 2020- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.12
CADD
Pathogenic
26
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.69
D
Eigen
Pathogenic
0.84
Eigen_PC
Pathogenic
0.79
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D
M_CAP
Uncertain
0.26
D
MetaRNN
Benign
0.077
T
MetaSVM
Uncertain
0.46
D
MutationAssessor
Pathogenic
3.6
H
PrimateAI
Uncertain
0.65
T
PROVEAN
Uncertain
-2.9
D
REVEL
Pathogenic
0.79
Sift
Uncertain
0.012
D
Sift4G
Uncertain
0.010
D
Polyphen
0.93
P
Vest4
0.93
MVP
0.90
MPC
0.54
ClinPred
0.057
T
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.

Other links and lift over

dbSNP: rs61755092; hg19: chr9-97329625; API