chr7-6009379-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006303.4(AIMP2):c.16G>C(p.Val6Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000821 in 1,611,826 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00084 ( 3 hom. )
Consequence
AIMP2
NM_006303.4 missense
NM_006303.4 missense
Scores
1
3
15
Clinical Significance
Conservation
PhyloP100: 6.14
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008596867).
BP6
?
Variant 7-6009379-G-C is Benign according to our data. Variant chr7-6009379-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 444713.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1}.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000838 (1223/1459496) while in subpopulation MID AF= 0.00603 (25/4148). AF 95% confidence interval is 0.00419. There are 3 homozygotes in gnomad4_exome. There are 636 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIMP2 | NM_006303.4 | c.16G>C | p.Val6Leu | missense_variant | 1/4 | ENST00000223029.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIMP2 | ENST00000223029.8 | c.16G>C | p.Val6Leu | missense_variant | 1/4 | 1 | NM_006303.4 | P1 | |
AIMP2 | ENST00000400479.6 | c.-251+1G>C | splice_donor_variant | 5 | |||||
AIMP2 | ENST00000395236.2 | c.16G>C | p.Val6Leu | missense_variant | 1/3 | 2 | |||
AIMP2 | ENST00000415999.1 | c.16G>C | p.Val6Leu | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000657 AC: 100AN: 152212Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00109 AC: 273AN: 250554Hom.: 2 AF XY: 0.00110 AC XY: 149AN XY: 135682
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GnomAD4 exome AF: 0.000838 AC: 1223AN: 1459496Hom.: 3 Cov.: 33 AF XY: 0.000876 AC XY: 636AN XY: 726046
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GnomAD4 genome ? AF: 0.000656 AC: 100AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74484
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at