chr5-894926-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004237.4(TRIP13):c.232A>G(p.Thr78Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004237.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.232A>G | p.Thr78Ala | missense_variant | Exon 2 of 13 | ENST00000166345.8 | NP_004228.1 | |
TRIP13 | NM_001166260.2 | c.232A>G | p.Thr78Ala | missense_variant | Exon 2 of 9 | NP_001159732.1 | ||
TRIP13 | XM_011514163.2 | c.232A>G | p.Thr78Ala | missense_variant | Exon 2 of 14 | XP_011512465.1 | ||
TRIP13 | XM_047417879.1 | c.-228A>G | 5_prime_UTR_variant | Exon 2 of 13 | XP_047273835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.232A>G | p.Thr78Ala | missense_variant | Exon 2 of 13 | 1 | NM_004237.4 | ENSP00000166345.3 | ||
TRIP13 | ENST00000512024.5 | n.347A>G | non_coding_transcript_exon_variant | Exon 2 of 9 | 1 | |||||
TRIP13 | ENST00000513435.1 | c.217A>G | p.Thr73Ala | missense_variant | Exon 2 of 8 | 5 | ENSP00000427528.1 | |||
TRIP13 | ENST00000508456.1 | n.206A>G | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 78 of the TRIP13 protein (p.Thr78Ala). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TRIP13-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at