1-20807343-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001391906.1(EIF4G3):ā€‹c.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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.74
Variant links:
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]

Genome browser will be placed here

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
EIF4G3NM_001391906.1 linkc.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
EIF4G3ENST00000602326.6 linkc.4902A>G p.Ala1634Ala synonymous_variant Exon 37 of 37 1 NM_001391906.1 ENSP00000473510.2 A0A8J9G7U8

Frequencies

GnomAD3 genomes
AF:
0.00572
AC:
871
AN:
152218
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00275
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00504
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00703
Gnomad FIN
AF:
0.00537
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00825
Gnomad OTH
AF:
0.00860
GnomAD3 exomes
AF:
0.00604
AC:
1505
AN:
249166
Hom.:
3
AF XY:
0.00653
AC XY:
879
AN XY:
134708
show subpopulations
Gnomad AFR exome
AF:
0.00321
Gnomad AMR exome
AF:
0.00367
Gnomad ASJ exome
AF:
0.00339
Gnomad EAS exome
AF:
0.0000547
Gnomad SAS exome
AF:
0.00783
Gnomad FIN exome
AF:
0.00610
Gnomad NFE exome
AF:
0.00763
Gnomad OTH exome
AF:
0.0104
GnomAD4 exome
AF:
0.00746
AC:
10837
AN:
1453516
Hom.:
52
Cov.:
30
AF XY:
0.00757
AC XY:
5463
AN XY:
722048
show subpopulations
Gnomad4 AFR exome
AF:
0.00261
Gnomad4 AMR exome
AF:
0.00409
Gnomad4 ASJ exome
AF:
0.00296
Gnomad4 EAS exome
AF:
0.0000254
Gnomad4 SAS exome
AF:
0.00782
Gnomad4 FIN exome
AF:
0.00603
Gnomad4 NFE exome
AF:
0.00812
Gnomad4 OTH exome
AF:
0.00771
GnomAD4 genome
AF:
0.00571
AC:
870
AN:
152336
Hom.:
4
Cov.:
32
AF XY:
0.00564
AC XY:
420
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.00274
Gnomad4 AMR
AF:
0.00503
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00683
Gnomad4 FIN
AF:
0.00537
Gnomad4 NFE
AF:
0.00825
Gnomad4 OTH
AF:
0.00851
Alfa
AF:
0.00696
Hom.:
2
Bravo
AF:
0.00533
Asia WGS
AF:
0.00289
AC:
10
AN:
3478

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
3.5
DANN
Benign
0.53

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: rs146669269; hg19: chr1-21133836; COSMIC: COSV99943990; API