5-893011-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_004237.4(TRIP13):c.13G>T(p.Val5Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000128 in 1,563,396 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
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.13G>T | p.Val5Leu | missense_variant | Exon 1 of 13 | ENST00000166345.8 | NP_004228.1 | |
TRIP13 | NM_001166260.2 | c.13G>T | p.Val5Leu | missense_variant | Exon 1 of 9 | NP_001159732.1 | ||
TRIP13 | XM_011514163.2 | c.13G>T | p.Val5Leu | missense_variant | Exon 1 of 14 | XP_011512465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.13G>T | p.Val5Leu | missense_variant | Exon 1 of 13 | 1 | NM_004237.4 | ENSP00000166345.3 | ||
TRIP13 | ENST00000512024.5 | n.128G>T | non_coding_transcript_exon_variant | Exon 1 of 9 | 1 | |||||
TRIP13 | ENST00000508456.1 | n.-14G>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 4AN: 149968Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000737 AC: 14AN: 189882Hom.: 0 AF XY: 0.0000478 AC XY: 5AN XY: 104656
GnomAD4 exome AF: 0.0000113 AC: 16AN: 1413428Hom.: 0 Cov.: 31 AF XY: 0.00000998 AC XY: 7AN XY: 701448
GnomAD4 genome AF: 0.0000267 AC: 4AN: 149968Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73192
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 5 of the TRIP13 protein (p.Val5Leu). This variant is present in population databases (rs759352780, gnomAD 0.05%). 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