chr11-7987468-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003754.3(EIF3F):c.116C>T(p.Pro39Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 1,605,270 control chromosomes in the GnomAD database, including 700 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003754.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF3F | NM_003754.3 | c.116C>T | p.Pro39Leu | missense_variant | 1/8 | ENST00000651655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF3F | ENST00000651655.1 | c.116C>T | p.Pro39Leu | missense_variant | 1/8 | NM_003754.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0382 AC: 5808AN: 152192Hom.: 147 Cov.: 33
GnomAD3 exomes AF: 0.0230 AC: 5353AN: 232710Hom.: 105 AF XY: 0.0215 AC XY: 2763AN XY: 128382
GnomAD4 exome AF: 0.0247 AC: 35855AN: 1452960Hom.: 552 Cov.: 31 AF XY: 0.0240 AC XY: 17326AN XY: 722892
GnomAD4 genome AF: 0.0382 AC: 5817AN: 152310Hom.: 148 Cov.: 33 AF XY: 0.0377 AC XY: 2805AN XY: 74478
ClinVar
Submissions by phenotype
EIF3F-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at