rs774103118
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001191061.2(SLC25A22):c.967G>A(p.Ala323Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000277 in 1,445,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001191061.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A22 | NM_001191061.2 | c.967G>A | p.Ala323Thr | missense_variant | 10/10 | ENST00000628067.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A22 | ENST00000628067.3 | c.967G>A | p.Ala323Thr | missense_variant | 10/10 | 1 | NM_001191061.2 | P1 | |
SLC25A22 | ENST00000320230.9 | c.967G>A | p.Ala323Thr | missense_variant | 10/10 | 1 | P1 | ||
SLC25A22 | ENST00000531214.5 | c.967G>A | p.Ala323Thr | missense_variant | 10/10 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000135 AC: 3AN: 222696Hom.: 0 AF XY: 0.0000243 AC XY: 3AN XY: 123570
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1445042Hom.: 0 Cov.: 31 AF XY: 0.00000556 AC XY: 4AN XY: 719052
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 323 of the SLC25A22 protein (p.Ala323Thr). This variant is present in population databases (rs774103118, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with SLC25A22-related conditions. ClinVar contains an entry for this variant (Variation ID: 461382). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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