11-126269217-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001425168.1(FOXRED1):c.-403G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,642 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 Uncertain significance (★).
Frequency
Consequence
NM_001425168.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152282Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250204Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135584
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461360Hom.: 0 Cov.: 37 AF XY: 0.00000963 AC XY: 7AN XY: 727024
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152282Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74400
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with methionine, which is neutral and non-polar, at codon 4 of the FOXRED1 protein (p.Arg4Met). This variant is present in population databases (rs146672359, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with FOXRED1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1380138). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt FOXRED1 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at