chr22-19176137-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_005984.5(SLC25A1):c.929C>T(p.Thr310Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,266 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T310A) has been classified as Uncertain significance.
Frequency
Consequence
NM_005984.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.929C>T | p.Thr310Met | missense_variant | 9/9 | ENST00000215882.10 | |
SLC25A1 | NM_001256534.2 | c.950C>T | p.Thr317Met | missense_variant | 8/8 | ||
SLC25A1 | NM_001287387.2 | c.620C>T | p.Thr207Met | missense_variant | 9/9 | ||
SLC25A1 | NR_046298.3 | n.853C>T | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.929C>T | p.Thr310Met | missense_variant | 9/9 | 1 | NM_005984.5 | P1 | |
SLC25A1 | ENST00000451283.5 | c.620C>T | p.Thr207Met | missense_variant | 9/9 | 2 | |||
SLC25A1 | ENST00000470922.5 | n.1071C>T | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251156Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135846
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461266Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726960
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2022 | This variant has not been reported in the literature in individuals affected with SLC25A1-related conditions. 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. 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"). This variant is present in population databases (rs782723670, gnomAD 0.009%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 310 of the SLC25A1 protein (p.Thr310Met). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at