chr5-900526-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004237.4(TRIP13):āc.421T>Cā(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 (ā ). 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.