5-893097-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_004237.4(TRIP13):c.92+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000189 in 1,583,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004237.4 splice_region, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.92+7C>T | splice_region_variant, intron_variant | Intron 1 of 12 | ENST00000166345.8 | NP_004228.1 | ||
TRIP13 | NM_001166260.2 | c.92+7C>T | splice_region_variant, intron_variant | Intron 1 of 8 | NP_001159732.1 | |||
TRIP13 | XM_011514163.2 | c.92+7C>T | splice_region_variant, intron_variant | Intron 1 of 13 | XP_011512465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.92+7C>T | splice_region_variant, intron_variant | Intron 1 of 12 | 1 | NM_004237.4 | ENSP00000166345.3 | |||
TRIP13 | ENST00000512024.5 | n.207+7C>T | splice_region_variant, intron_variant | Intron 1 of 8 | 1 | |||||
TRIP13 | ENST00000508456.1 | n.66+7C>T | splice_region_variant, intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000205 AC: 4AN: 194988Hom.: 0 AF XY: 0.00000934 AC XY: 1AN XY: 107016
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1431170Hom.: 0 Cov.: 31 AF XY: 0.0000197 AC XY: 14AN XY: 710278
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74408
ClinVar
Submissions by phenotype
TRIP13-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at