1-21003621-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001391906.1(EIF4G3):c.-66-813C>G variant causes a intron change. The variant allele was found at a frequency of 0.0205 in 326,596 control chromosomes in the GnomAD database, including 105 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 0.020 ( 60 hom., cov: 32)
Exomes 𝑓: 0.020 ( 45 hom. )
Consequence
EIF4G3
NM_001391906.1 intron
NM_001391906.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.78
Genes affected
EIF4G3 (HGNC:3298): (eukaryotic translation initiation factor 4 gamma 3) The protein encoded by this gene is thought to be part of the eIF4F protein complex, which is involved in mRNA cap recognition and transport of mRNAs to the ribosome. Interestingly, a microRNA (miR-520c-3p) has been found that negatively regulates synthesis of the encoded protein, and this leads to a global decrease in protein translation and cell proliferation. Therefore, this protein is a key component of the anti-tumor activity of miR-520c-3p. [provided by RefSeq, May 2016]
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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=-0.52).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0205 (3117/152210) while in subpopulation NFE AF= 0.0265 (1805/68010). AF 95% confidence interval is 0.0255. There are 60 homozygotes in gnomad4. There are 1604 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 60 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EIF4G3 | NM_001391906.1 | c.-66-813C>G | intron_variant | Intron 4 of 36 | ENST00000602326.6 | NP_001378835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF4G3 | ENST00000602326.6 | c.-66-813C>G | intron_variant | Intron 4 of 36 | 1 | NM_001391906.1 | ENSP00000473510.2 | |||
EIF4G3 | ENST00000356916.7 | c.-66-813C>G | intron_variant | Intron 6 of 14 | 1 | ENSP00000349386.3 |
Frequencies
GnomAD3 genomes AF: 0.0205 AC: 3121AN: 152090Hom.: 60 Cov.: 32
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GnomAD4 exome AF: 0.0205 AC: 3569AN: 174386Hom.: 45 Cov.: 0 AF XY: 0.0194 AC XY: 1989AN XY: 102662
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GnomAD4 genome AF: 0.0205 AC: 3117AN: 152210Hom.: 60 Cov.: 32 AF XY: 0.0216 AC XY: 1604AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at