11-65883997-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_004214.5(FIBP):​c.1051C>T​(p.Leu351Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

FIBP
NM_004214.5 missense

Scores

7
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.25
Variant links:
Genes affected
FIBP (HGNC:3705): (FGF1 intracellular binding protein) Acidic fibroblast growth factor is mitogenic for a variety of different cell types and acts by stimulating mitogenesis or inducing morphological changes and differentiation. The FIBP protein is an intracellular protein that binds selectively to acidic fibroblast growth factor (aFGF). It is postulated that FIBP may be involved in the mitogenic action of aFGF. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.38528362).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FIBPNM_004214.5 linkc.1051C>T p.Leu351Phe missense_variant Exon 10 of 10 ENST00000357519.9 NP_004205.2 O43427-2
FIBPNM_198897.2 linkc.1072C>T p.Leu358Phe missense_variant Exon 10 of 10 NP_942600.1 O43427-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FIBPENST00000357519.9 linkc.1051C>T p.Leu351Phe missense_variant Exon 10 of 10 1 NM_004214.5 ENSP00000350124.5 O43427-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000120
AC:
3
AN:
249434
Hom.:
0
AF XY:
0.0000148
AC XY:
2
AN XY:
135072
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.0000655
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461708
Hom.:
0
Cov.:
32
AF XY:
0.00000550
AC XY:
4
AN XY:
727152
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378
ExAC
AF:
0.0000247
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Sep 26, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1072C>T (p.L358F) alteration is located in exon 10 (coding exon 10) of the FIBP gene. This alteration results from a C to T substitution at nucleotide position 1072, causing the leucine (L) at amino acid position 358 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.40
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.36
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.097
T;.
Eigen
Benign
-0.061
Eigen_PC
Benign
0.066
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.81
T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.39
T;T
MetaSVM
Benign
-0.83
T
MutationAssessor
Benign
1.8
L;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-1.9
N;N
REVEL
Benign
0.14
Sift
Uncertain
0.0080
D;D
Sift4G
Uncertain
0.044
D;D
Polyphen
0.85
P;P
Vest4
0.28
MutPred
0.61
Loss of helix (P = 0.0196);.;
MVP
0.34
MPC
1.1
ClinPred
0.66
D
GERP RS
3.9
Varity_R
0.25
gMVP
0.41

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: rs746692808; hg19: chr11-65651468; API