7-6023401-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006303.4(AIMP2):c.673C>G(p.His225Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,614,084 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIMP2 | NM_006303.4 | c.673C>G | p.His225Asp | missense_variant | Exon 4 of 4 | ENST00000223029.8 | NP_006294.2 | |
EIF2AK1 | NM_014413.4 | c.*1272G>C | 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.673C>G | p.His225Asp | missense_variant | Exon 4 of 4 | 1 | NM_006303.4 | ENSP00000223029.3 | ||
EIF2AK1 | ENST00000199389 | c.*1272G>C | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_014413.4 | ENSP00000199389.6 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250244Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135356
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461892Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1948769). This variant has not been reported in the literature in individuals affected with AIMP2-related conditions. This variant is present in population databases (rs369386259, gnomAD 0.03%). This sequence change replaces histidine, which is basic and polar, with aspartic acid, which is acidic and polar, at codon 225 of the AIMP2 protein (p.His225Asp). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at