chr5-914504-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_004237.4(TRIP13):c.1060C>T(p.Arg354Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,282 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
TRIP13
NM_004237.4 stop_gained
NM_004237.4 stop_gained
Scores
2
3
2
Clinical Significance
Conservation
PhyloP100: 1.07
Genes affected
TRIP13 (HGNC:12307): (thyroid hormone receptor interactor 13) This gene encodes a protein that interacts with thyroid hormone receptors, also known as hormone-dependent transcription factors. The gene product interacts specifically with the ligand binding domain. This gene is one of several that may play a role in early-stage non-small cell lung cancer. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 5-914504-C-T is Pathogenic according to our data. Variant chr5-914504-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 431045.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.1060C>T | p.Arg354Ter | stop_gained | 11/13 | ENST00000166345.8 | |
TRIP13 | XM_011514163.2 | c.1060C>T | p.Arg354Ter | stop_gained | 11/14 | ||
TRIP13 | XM_047417879.1 | c.601C>T | p.Arg201Ter | stop_gained | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.1060C>T | p.Arg354Ter | stop_gained | 11/13 | 1 | NM_004237.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461282Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726978
GnomAD4 exome
AF:
AC:
3
AN:
1461282
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Cov.:
31
AF XY:
AC XY:
2
AN XY:
726978
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mosaic variegated aneuploidy syndrome 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 27, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
MutationTaster
Benign
A
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: -39
Find out detailed SpliceAI scores and Pangolin per-transcript scores at