chr11-7987407-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003754.3(EIF3F):c.55C>T(p.Pro19Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,600,868 control chromosomes in the GnomAD database, including 1 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 Likely benign (★).
Frequency
Consequence
NM_003754.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF3F | NM_003754.3 | c.55C>T | p.Pro19Ser | missense_variant | 1/8 | ENST00000651655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF3F | ENST00000651655.1 | c.55C>T | p.Pro19Ser | missense_variant | 1/8 | NM_003754.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 176AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000328 AC: 76AN: 231464Hom.: 0 AF XY: 0.000282 AC XY: 36AN XY: 127828
GnomAD4 exome AF: 0.000112 AC: 162AN: 1448518Hom.: 1 Cov.: 31 AF XY: 0.0000957 AC XY: 69AN XY: 721008
GnomAD4 genome AF: 0.00116 AC: 176AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.00109 AC XY: 81AN XY: 74502
ClinVar
Submissions by phenotype
EIF3F-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at