rs782004176
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_005984.5(SLC25A1):c.776C>T(p.Thr259Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T259T) has been classified as Likely benign.
Frequency
Consequence
NM_005984.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.776C>T | p.Thr259Met | missense_variant | 8/9 | ENST00000215882.10 | |
SLC25A1 | NM_001256534.2 | c.797C>T | p.Thr266Met | missense_variant | 7/8 | ||
SLC25A1 | NM_001287387.2 | c.467C>T | p.Thr156Met | missense_variant | 8/9 | ||
SLC25A1 | NR_046298.3 | n.700C>T | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.776C>T | p.Thr259Met | missense_variant | 8/9 | 1 | NM_005984.5 | P1 | |
SLC25A1 | ENST00000451283.5 | c.467C>T | p.Thr156Met | missense_variant | 8/9 | 2 | |||
SLC25A1 | ENST00000470922.5 | n.918C>T | non_coding_transcript_exon_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251394Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461558Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727090
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 12, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at