11-7987486-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
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 (no stars).
Frequency
Consequence
NM_003754.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00108 AC: 253AN: 233974Hom.: 3 AF XY: 0.00101 AC XY: 130AN XY: 128848
GnomAD4 exome AF: 0.000570 AC: 829AN: 1454020Hom.: 4 Cov.: 31 AF XY: 0.000593 AC XY: 429AN XY: 723110
GnomAD4 genome AF: 0.000551 AC: 84AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74500
ClinVar
Submissions by phenotype
EIF3F-related disorder Benign:1
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