chr12-109911075-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001143852.2(TCHP):c.892C>T(p.Arg298Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000114 in 1,581,538 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R298Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001143852.2 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCHP | NM_001143852.2 | c.892C>T | p.Arg298Trp | missense_variant | 9/13 | ENST00000405876.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCHP | ENST00000405876.9 | c.892C>T | p.Arg298Trp | missense_variant | 9/13 | 1 | NM_001143852.2 | P1 | |
TCHP | ENST00000312777.9 | c.892C>T | p.Arg298Trp | missense_variant | 9/13 | 1 | P1 | ||
TCHP | ENST00000549550.1 | n.136C>T | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
TCHP | ENST00000544838.5 | c.892C>T | p.Arg298Trp | missense_variant, NMD_transcript_variant | 9/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000479 AC: 1AN: 208632Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113620
GnomAD4 exome AF: 0.0000119 AC: 17AN: 1429328Hom.: 0 Cov.: 30 AF XY: 0.0000127 AC XY: 9AN XY: 707978
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.892C>T (p.R298W) alteration is located in exon 9 (coding exon 8) of the TCHP gene. This alteration results from a C to T substitution at nucleotide position 892, causing the arginine (R) at amino acid position 298 to be replaced by a tryptophan (W). 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