chr3-184319426-GGT-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_198241.3(EIF4G1):c.425-224_425-223del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.029 ( 36 hom., cov: 0)
Consequence
EIF4G1
NM_198241.3 intron
NM_198241.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.764
Genes affected
EIF4G1 (HGNC:3296): (eukaryotic translation initiation factor 4 gamma 1) The protein encoded by this gene is a component of the multi-subunit protein complex EIF4F. This complex facilitates the recruitment of mRNA to the ribosome, which is a rate-limiting step during the initiation phase of protein synthesis. The recognition of the mRNA cap and the ATP-dependent unwinding of 5'-terminal secondary structure is catalyzed by factors in this complex. The subunit encoded by this gene is a large scaffolding protein that contains binding sites for other members of the EIF4F complex. A domain at its N-terminus can also interact with the poly(A)-binding protein, which may mediate the circularization of mRNA during translation. Alternative splicing results in multiple transcript variants, some of which are derived from alternative promoter usage. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 3-184319426-GGT-G is Benign according to our data. Variant chr3-184319426-GGT-G is described in ClinVar as [Benign]. Clinvar id is 1183465.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0292 (3301/112874) while in subpopulation EAS AF= 0.0513 (210/4096). AF 95% confidence interval is 0.0456. There are 36 homozygotes in gnomad4. There are 1632 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3297 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF4G1 | NM_198241.3 | c.425-224_425-223del | intron_variant | ENST00000346169.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF4G1 | ENST00000346169.7 | c.425-224_425-223del | intron_variant | 1 | NM_198241.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0292 AC: 3297AN: 112786Hom.: 36 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0292 AC: 3301AN: 112874Hom.: 36 Cov.: 0 AF XY: 0.0302 AC XY: 1632AN XY: 54116
GnomAD4 genome
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3301
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54116
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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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