7-6023408-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006303.4(AIMP2):c.680C>T(p.Ala227Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,884 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_006303.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIMP2 | NM_006303.4 | c.680C>T | p.Ala227Val | missense_variant | Exon 4 of 4 | ENST00000223029.8 | NP_006294.2 | |
EIF2AK1 | NM_014413.4 | c.*1265G>A | 3_prime_UTR_variant | Exon 15 of 15 | ENST00000199389.11 | NP_055228.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AIMP2 | ENST00000223029.8 | c.680C>T | p.Ala227Val | missense_variant | Exon 4 of 4 | 1 | NM_006303.4 | ENSP00000223029.3 | ||
EIF2AK1 | ENST00000199389 | c.*1265G>A | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_014413.4 | ENSP00000199389.6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250016Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135250
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461884Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727242
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with AIMP2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 227 of the AIMP2 protein (p.Ala227Val). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at