7-6009342-C-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006303.4(AIMP2):c.-22C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 1,611,438 control chromosomes in the GnomAD database, including 38,291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).
Frequency
Genomes: 𝑓 0.24 ( 4559 hom., cov: 32)
Exomes 𝑓: 0.21 ( 33732 hom. )
Consequence
AIMP2
NM_006303.4 5_prime_UTR
NM_006303.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.387
Genes affected
AIMP2 (HGNC:20609): (aminoacyl tRNA synthetase complex interacting multifunctional protein 2) The protein encoded by this gene is part of the aminoacyl-tRNA synthetase complex, which contains nine different aminoacyl-tRNA synthetases and three non-enzymatic factors. The encoded protein is one of the non-enzymatic factors and is required for assembly and stability of the complex. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 7-6009342-C-A is Benign according to our data. Variant chr7-6009342-C-A is described in ClinVar as [Benign]. Clinvar id is 91284.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr7-6009342-C-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AIMP2 | NM_006303.4 | c.-22C>A | 5_prime_UTR_variant | 1/4 | ENST00000223029.8 | NP_006294.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.236 AC: 35864AN: 151960Hom.: 4553 Cov.: 32
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GnomAD3 exomes AF: 0.211 AC: 52714AN: 250350Hom.: 6004 AF XY: 0.212 AC XY: 28778AN XY: 135620
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GnomAD4 exome AF: 0.212 AC: 308709AN: 1459360Hom.: 33732 Cov.: 34 AF XY: 0.212 AC XY: 154060AN XY: 725994
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GnomAD4 genome AF: 0.236 AC: 35873AN: 152078Hom.: 4559 Cov.: 32 AF XY: 0.237 AC XY: 17655AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Lynch syndrome Benign:1
Benign, reviewed by expert panel | research | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Sep 05, 2013 | MAF >1% - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at