chr7-6009406-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006303.4(AIMP2):āc.43C>Gā(p.Pro15Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,611,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006303.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIMP2 | NM_006303.4 | c.43C>G | p.Pro15Ala | missense_variant | 1/4 | ENST00000223029.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIMP2 | ENST00000223029.8 | c.43C>G | p.Pro15Ala | missense_variant | 1/4 | 1 | NM_006303.4 | P1 | |
AIMP2 | ENST00000395236.2 | c.43C>G | p.Pro15Ala | missense_variant | 1/3 | 2 | |||
AIMP2 | ENST00000400479.6 | c.-251+28C>G | intron_variant | 5 | |||||
AIMP2 | ENST00000415999.1 | c.43C>G | p.Pro15Ala | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250168Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135576
GnomAD4 exome AF: 0.000108 AC: 157AN: 1459308Hom.: 0 Cov.: 32 AF XY: 0.000113 AC XY: 82AN XY: 725964
GnomAD4 genome AF: 0.000138 AC: 21AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 24, 2022 | This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 15 of the AIMP2 protein (p.Pro15Ala). This variant is present in population databases (rs145891242, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with AIMP2-related conditions. 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. 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