chr22-41469172-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001098.3(ACO2):c.26C>T(p.Thr9Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000522 in 1,608,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACO2 | NM_001098.3 | c.26C>T | p.Thr9Ile | missense_variant | 1/18 | ENST00000216254.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACO2 | ENST00000216254.9 | c.26C>T | p.Thr9Ile | missense_variant | 1/18 | 1 | NM_001098.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152258Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000447 AC: 11AN: 245828Hom.: 0 AF XY: 0.0000376 AC XY: 5AN XY: 133006
GnomAD4 exome AF: 0.0000522 AC: 76AN: 1456236Hom.: 0 Cov.: 31 AF XY: 0.0000497 AC XY: 36AN XY: 724402
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152376Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74514
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 9 of the ACO2 protein (p.Thr9Ile). This variant is present in population databases (rs146048865, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with ACO2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1019555). 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. 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