chr22-43159279-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000714.6(TSPO):c.41C>T(p.Ala14Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,556,046 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000714.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPO | NM_000714.6 | c.41C>T | p.Ala14Val | missense_variant | 2/4 | ENST00000337554.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPO | ENST00000337554.8 | c.41C>T | p.Ala14Val | missense_variant | 2/4 | 1 | NM_000714.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00151 AC: 230AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 250AN: 155014Hom.: 1 AF XY: 0.00168 AC XY: 140AN XY: 83254
GnomAD4 exome AF: 0.00249 AC: 3499AN: 1403718Hom.: 6 Cov.: 32 AF XY: 0.00250 AC XY: 1734AN XY: 693284
GnomAD4 genome ? AF: 0.00152 AC: 231AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.00142 AC XY: 106AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at