6-41043055-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001010873.3(TSPO2):c.70C>T(p.Arg24Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,874 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. R24H) has been classified as Likely benign.
Frequency
Consequence
NM_001010873.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPO2 | NM_001010873.3 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | ENST00000373161.6 | NP_001010873.1 | |
TSPO2 | NM_001159726.1 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | NP_001153198.1 | ||
TSPO2 | XM_011514396.3 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | XP_011512698.1 | ||
TSPO2 | XM_011514397.3 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | XP_011512699.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPO2 | ENST00000373161.6 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | 1 | NM_001010873.3 | ENSP00000362255.1 | ||
TSPO2 | ENST00000470917.1 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 4 | 1 | ENSP00000419985.1 | |||
TSPO2 | ENST00000373158.6 | c.70C>T | p.Arg24Cys | missense_variant | Exon 2 of 3 | 1 | ENSP00000362252.2 | |||
OARD1 | ENST00000482853.5 | n.*13-7920G>A | intron_variant | Intron 3 of 4 | 2 | ENSP00000420472.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.70C>T (p.R24C) alteration is located in exon 2 (coding exon 1) of the TSPO2 gene. This alteration results from a C to T substitution at nucleotide position 70, causing the arginine (R) at amino acid position 24 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.