chr6-41043056-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001010873.3(TSPO2):c.71G>A(p.Arg24His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 1,614,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R24C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001010873.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPO2 | NM_001010873.3 | c.71G>A | p.Arg24His | missense_variant | 2/4 | ENST00000373161.6 | |
TSPO2 | NM_001159726.1 | c.71G>A | p.Arg24His | missense_variant | 2/4 | ||
TSPO2 | XM_011514396.3 | c.71G>A | p.Arg24His | missense_variant | 2/4 | ||
TSPO2 | XM_011514397.3 | c.71G>A | p.Arg24His | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPO2 | ENST00000373161.6 | c.71G>A | p.Arg24His | missense_variant | 2/4 | 1 | NM_001010873.3 | P1 | |
TSPO2 | ENST00000470917.1 | c.71G>A | p.Arg24His | missense_variant | 2/4 | 1 | P1 | ||
TSPO2 | ENST00000373158.6 | c.71G>A | p.Arg24His | missense_variant | 2/3 | 1 | |||
OARD1 | ENST00000482853.5 | c.*13-7921C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000421 AC: 64AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 251374Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135828
GnomAD4 exome AF: 0.0000540 AC: 79AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727246
GnomAD4 genome ? AF: 0.000420 AC: 64AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74424
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at