rs4677039
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134651.2(EIF4E3):c.249+2798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,828 control chromosomes in the GnomAD database, including 6,093 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 6093 hom., cov: 31)
Consequence
EIF4E3
NM_001134651.2 intron
NM_001134651.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.01
Genes affected
EIF4E3 (HGNC:31837): (eukaryotic translation initiation factor 4E family member 3) EIF4E3 belongs to the EIF4E family of translational initiation factors that interact with the 5-prime cap structure of mRNA and recruit mRNA to the ribosome (Joshi et al., 2004 [PubMed 15153109]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF4E3 | NM_001134651.2 | c.249+2798G>A | intron_variant | ENST00000425534.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF4E3 | ENST00000425534.8 | c.249+2798G>A | intron_variant | 2 | NM_001134651.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.261 AC: 39617AN: 151710Hom.: 6092 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.261 AC: 39618AN: 151828Hom.: 6093 Cov.: 31 AF XY: 0.264 AC XY: 19607AN XY: 74196
GnomAD4 genome
?
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39618
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151828
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31
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19607
AN XY:
74196
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858
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at