4-106325080-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142416.2(AIMP1):c.71A>T(p.Tyr24Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,612,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001142416.2 missense
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: 0.0000854 AC: 13AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250778Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135588
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460810Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726732
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.71A>T (p.Y24F) alteration is located in exon 2 (coding exon 1) of the AIMP1 gene. This alteration results from a A to T substitution at nucleotide position 71, causing the tyrosine (Y) at amino acid position 24 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 24 of the AIMP1 protein (p.Tyr24Phe). This variant is present in population databases (rs369840696, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with AIMP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1431757). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The phenylalanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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