GeneBe

4-119320747-T-A

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000134.4(FABP2):​c.163A>T​(p.Thr55Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T55A) has been classified as Benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

FABP2
NM_000134.4 missense

Scores

1
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.413

Publications

287 publications found
Variant links:
Genes affected
FABP2 (HGNC:3556): (fatty acid binding protein 2) The protein encoded by this gene is an intracellular fatty acid-binding protein that participates in the uptake, intracellular metabolism, and transport of long-chain fatty acids. The encoded protein is also involved in the modulation of cell growth and proliferation. This protein binds saturated long-chain fatty acids with high affinity, and may act as a lipid sensor to maintain energy homeostasis. [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14223051).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000134.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FABP2
NM_000134.4
MANE Select
c.163A>Tp.Thr55Ser
missense
Exon 2 of 4NP_000125.2P12104

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
FABP2
ENST00000274024.4
TSL:1 MANE Select
c.163A>Tp.Thr55Ser
missense
Exon 2 of 4ENSP00000274024.3P12104
ENSG00000294020
ENST00000720595.1
n.176-13581T>A
intron
N/A
ENSG00000294020
ENST00000720596.1
n.224-13581T>A
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1454356
Hom.:
0
Cov.:
38
AF XY:
0.00
AC XY:
0
AN XY:
723480
African (AFR)
AF:
0.00
AC:
0
AN:
32898
American (AMR)
AF:
0.00
AC:
0
AN:
43198
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26010
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39270
South Asian (SAS)
AF:
0.00
AC:
0
AN:
84786
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53116
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5704
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1109310
Other (OTH)
AF:
0.00
AC:
0
AN:
60064
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
114164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.16
DANN
Benign
0.62
Eigen
Benign
-0.91
Eigen_PC
Benign
-0.95
FATHMM_MKL
Benign
0.44
N
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.14
T
MetaSVM
Benign
-0.95
T
PhyloP100
0.41
PrimateAI
Benign
0.24
T
PROVEAN
Uncertain
-2.8
D
REVEL
Benign
0.049
Sift
Benign
0.18
T
Sift4G
Benign
0.32
T
Vest4
0.17
MutPred
0.63
Gain of disorder (P = 0.0398)
MVP
0.061
MPC
0.093
ClinPred
0.13
T
GERP RS
0.048
gMVP
0.42
Mutation Taster
=95/5
polymorphism

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

Other links and lift over

dbSNP: rs1799883; hg19: chr4-120241902; API