12-109911205-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143852.2(TCHP):c.1022C>T(p.Ala341Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,584,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143852.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCHP | NM_001143852.2 | c.1022C>T | p.Ala341Val | missense_variant | 9/13 | ENST00000405876.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCHP | ENST00000405876.9 | c.1022C>T | p.Ala341Val | missense_variant | 9/13 | 1 | NM_001143852.2 | P1 | |
TCHP | ENST00000312777.9 | c.1022C>T | p.Ala341Val | missense_variant | 9/13 | 1 | P1 | ||
TCHP | ENST00000549550.1 | n.266C>T | non_coding_transcript_exon_variant | 2/4 | 3 | ||||
TCHP | ENST00000544838.5 | c.1022C>T | p.Ala341Val | missense_variant, NMD_transcript_variant | 9/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 25AN: 206412Hom.: 0 AF XY: 0.000117 AC XY: 13AN XY: 111506
GnomAD4 exome AF: 0.000115 AC: 164AN: 1431874Hom.: 0 Cov.: 30 AF XY: 0.000111 AC XY: 79AN XY: 709732
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2023 | The c.1022C>T (p.A341V) 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 1022, causing the alanine (A) at amino acid position 341 to be replaced by a valine (V). 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