chr11-7987628-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_003754.3(EIF3F):āc.276C>Gā(p.Val92=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,576,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 33)
Exomes š: 0.000027 ( 0 hom. )
Consequence
EIF3F
NM_003754.3 synonymous
NM_003754.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.37
Genes affected
EIF3F (HGNC:3275): (eukaryotic translation initiation factor 3 subunit F) Enables deubiquitinase activity and identical protein binding activity. Contributes to translation initiation factor activity. Involved in IRES-dependent viral translational initiation; protein deubiquitination; and translational initiation. Located in membrane. Part of eukaryotic translation initiation factor 3 complex. Implicated in autosomal recessive non-syndromic intellectual disability. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 11-7987628-C-G is Benign according to our data. Variant chr11-7987628-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2641577.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.37 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF3F | NM_003754.3 | c.276C>G | p.Val92= | synonymous_variant | 1/8 | ENST00000651655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF3F | ENST00000651655.1 | c.276C>G | p.Val92= | synonymous_variant | 1/8 | NM_003754.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000229 AC: 5AN: 218278Hom.: 0 AF XY: 0.0000252 AC XY: 3AN XY: 118872
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GnomAD4 exome AF: 0.0000274 AC: 39AN: 1424588Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 19AN XY: 704420
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
EIF3F-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | EIF3F: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at