rs201302296

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001130679.3(EIF4E):​c.415A>T​(p.Met139Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000468 in 426,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

EIF4E
NM_001130679.3 missense

Scores

15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.792
Variant links:
Genes affected
EIF4E (HGNC:3287): (eukaryotic translation initiation factor 4E) The protein encoded by this gene is a component of the eukaryotic translation initiation factor 4F complex, which recognizes the 7-methylguanosine cap structure at the 5' end of messenger RNAs. The encoded protein aids in translation initiation by recruiting ribosomes to the 5'-cap structure. Association of this protein with the 4F complex is the rate-limiting step in translation initiation. This gene acts as a proto-oncogene, and its expression and activation is associated with transformation and tumorigenesis. Several pseudogenes of this gene are found on other chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.073277354).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EIF4ENM_001968.5 linkc.399+548A>T intron_variant Intron 5 of 6 ENST00000450253.7 NP_001959.1 P06730-1
EIF4ENM_001130679.3 linkc.415A>T p.Met139Leu missense_variant Exon 6 of 8 NP_001124151.1 P06730-2
EIF4ENM_001331017.2 linkc.483+548A>T intron_variant Intron 6 of 7 NP_001317946.1 P06730D6RBW1
EIF4ENM_001130678.4 linkc.459+548A>T intron_variant Intron 5 of 6 NP_001124150.1 P06730-3Q32Q75X5D7E3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EIF4EENST00000450253.7 linkc.399+548A>T intron_variant Intron 5 of 6 1 NM_001968.5 ENSP00000389624.2 P06730-1

Frequencies

GnomAD3 genomes
AF:
0.00000659
AC:
1
AN:
151656
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000363
AC:
1
AN:
275152
Hom.:
0
Cov.:
0
AF XY:
0.00000642
AC XY:
1
AN XY:
155812
show subpopulations
Gnomad4 AFR exome
AF:
0.000133
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000659
AC:
1
AN:
151774
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74166
show subpopulations
Gnomad4 AFR
AF:
0.0000242
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000648
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
0.48
DANN
Benign
0.23
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.8
FATHMM_MKL
Benign
0.0097
N
LIST_S2
Benign
0.50
T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.073
T
MetaSVM
Benign
-1.0
T
PROVEAN
Benign
0.020
N
REVEL
Benign
0.023
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.19
MutPred
0.58
Loss of solvent accessibility (P = 0.0249);
MVP
0.39
MPC
1.1
ClinPred
0.069
T
GERP RS
-1.8
gMVP
0.71

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: rs201302296; hg19: chr4-99807682; API