X-54440746-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_058163.3(TSR2):āc.138G>Cā(p.Leu46Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000915 in 1,202,198 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_058163.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSR2 | NM_058163.3 | c.138G>C | p.Leu46Leu | synonymous_variant | Exon 2 of 5 | ENST00000375151.5 | NP_477511.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000626 AC: 7AN: 111743Hom.: 0 Cov.: 23 AF XY: 0.0000884 AC XY: 3AN XY: 33929
GnomAD3 exomes AF: 0.00000585 AC: 1AN: 170800Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 56996
GnomAD4 exome AF: 0.00000367 AC: 4AN: 1090455Hom.: 0 Cov.: 30 AF XY: 0.00000561 AC XY: 2AN XY: 356757
GnomAD4 genome AF: 0.0000626 AC: 7AN: 111743Hom.: 0 Cov.: 23 AF XY: 0.0000884 AC XY: 3AN XY: 33929
ClinVar
Submissions by phenotype
not provided Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 2191008). 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. This variant has not been reported in the literature in individuals affected with TSR2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.004%). This sequence change affects codon 46 of the TSR2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the TSR2 protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at