22-26541329-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_003595.5(TPST2):c.302G>T(p.Arg101Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000349 in 1,547,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003595.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPST2 | NM_003595.5 | c.302G>T | p.Arg101Leu | missense_variant | 3/7 | ENST00000338754.9 | NP_003586.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPST2 | ENST00000338754.9 | c.302G>T | p.Arg101Leu | missense_variant | 3/7 | 1 | NM_003595.5 | ENSP00000339813.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000203 AC: 4AN: 197346Hom.: 0 AF XY: 0.00000951 AC XY: 1AN XY: 105190
GnomAD4 exome AF: 0.0000373 AC: 52AN: 1395336Hom.: 0 Cov.: 73 AF XY: 0.0000306 AC XY: 21AN XY: 685940
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2024 | The c.302G>T (p.R101L) alteration is located in exon 3 (coding exon 1) of the TPST2 gene. This alteration results from a G to T substitution at nucleotide position 302, causing the arginine (R) at amino acid position 101 to be replaced by a leucine (L). 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