chr11-7987486-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003754.3(EIF3F):c.134C>T(p.Ser45Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000568 in 1,606,384 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00055 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00057 ( 4 hom. )
Consequence
EIF3F
NM_003754.3 missense
NM_003754.3 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 2.68
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0036212504).
BP6
Variant 11-7987486-C-T is Benign according to our data. Variant chr11-7987486-C-T is described in ClinVar as [Benign]. Clinvar id is 3033107.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF3F | NM_003754.3 | c.134C>T | p.Ser45Leu | missense_variant | 1/8 | ENST00000651655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF3F | ENST00000651655.1 | c.134C>T | p.Ser45Leu | missense_variant | 1/8 | NM_003754.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152246Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00108 AC: 253AN: 233974Hom.: 3 AF XY: 0.00101 AC XY: 130AN XY: 128848
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GnomAD4 exome AF: 0.000570 AC: 829AN: 1454020Hom.: 4 Cov.: 31 AF XY: 0.000593 AC XY: 429AN XY: 723110
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GnomAD4 genome AF: 0.000551 AC: 84AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EIF3F-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Benign
T;T;.
Sift4G
Benign
T;T;.
Polyphen
B;B;.
Vest4
MutPred
Loss of glycosylation at S45 (P = 5e-04);Loss of glycosylation at S45 (P = 5e-04);Loss of glycosylation at S45 (P = 5e-04);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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