5-900526-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004237.4(TRIP13):c.421T>C(p.Tyr141His) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,459,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Y141Y) has been classified as Likely benign.
Frequency
Consequence
NM_004237.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.421T>C | p.Tyr141His | missense_variant | 4/13 | ENST00000166345.8 | |
TRIP13 | NM_001166260.2 | c.421T>C | p.Tyr141His | missense_variant | 4/9 | ||
TRIP13 | XM_011514163.2 | c.421T>C | p.Tyr141His | missense_variant | 4/14 | ||
TRIP13 | XM_047417879.1 | c.-39T>C | 5_prime_UTR_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.421T>C | p.Tyr141His | missense_variant | 4/13 | 1 | NM_004237.4 | P1 | |
TRIP13 | ENST00000512024.5 | n.536T>C | non_coding_transcript_exon_variant | 4/9 | 1 | ||||
TRIP13 | ENST00000513435.1 | c.409T>C | p.Tyr137His | missense_variant | 4/8 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459602Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726098
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.421T>C (p.Y141H) alteration is located in exon 4 (coding exon 4) of the TRIP13 gene. This alteration results from a T to C substitution at nucleotide position 421, causing the tyrosine (Y) at amino acid position 141 to be replaced by a histidine (H). 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
Publications
No publications associated with this variant yet.