chrX-54440751-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001346790.2(TSR2):c.-245G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 111,731 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001346790.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSR2 | NM_058163.3 | c.143G>T | p.Gly48Val | missense_variant | Exon 2 of 5 | ENST00000375151.5 | NP_477511.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000895 AC: 1AN: 111731Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33883
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000895 AC: 1AN: 111731Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33883
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at