1-20807343-T-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001391906.1(EIF4G3):āc.4902A>Gā(p.Ala1634Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00729 in 1,605,852 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0057 ( 4 hom., cov: 32)
Exomes š: 0.0075 ( 52 hom. )
Consequence
EIF4G3
NM_001391906.1 synonymous
NM_001391906.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.74
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-20807343-T-C is Benign according to our data. Variant chr1-20807343-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638442.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.74 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EIF4G3 | NM_001391906.1 | c.4902A>G | p.Ala1634Ala | synonymous_variant | Exon 37 of 37 | ENST00000602326.6 | NP_001378835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EIF4G3 | ENST00000602326.6 | c.4902A>G | p.Ala1634Ala | synonymous_variant | Exon 37 of 37 | 1 | NM_001391906.1 | ENSP00000473510.2 |
Frequencies
GnomAD3 genomes AF: 0.00572 AC: 871AN: 152218Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00604 AC: 1505AN: 249166Hom.: 3 AF XY: 0.00653 AC XY: 879AN XY: 134708
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GnomAD4 exome AF: 0.00746 AC: 10837AN: 1453516Hom.: 52 Cov.: 30 AF XY: 0.00757 AC XY: 5463AN XY: 722048
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GnomAD4 genome AF: 0.00571 AC: 870AN: 152336Hom.: 4 Cov.: 32 AF XY: 0.00564 AC XY: 420AN XY: 74494
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
EIF4G3: BP4, BP7, BS2 -
Computational scores
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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