chr5-896670-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004237.4(TRIP13):c.264C>T(p.Ile88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000834 in 1,606,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000088 ( 0 hom. )
Consequence
TRIP13
NM_004237.4 synonymous
NM_004237.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.821
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP7
Synonymous conserved (PhyloP=-0.821 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.264C>T | p.Ile88= | synonymous_variant | 3/13 | ENST00000166345.8 | |
TRIP13 | NM_001166260.2 | c.264C>T | p.Ile88= | synonymous_variant | 3/9 | ||
TRIP13 | XM_011514163.2 | c.264C>T | p.Ile88= | synonymous_variant | 3/14 | ||
TRIP13 | XM_047417879.1 | c.-196C>T | 5_prime_UTR_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.264C>T | p.Ile88= | synonymous_variant | 3/13 | 1 | NM_004237.4 | P1 | |
TRIP13 | ENST00000512024.5 | n.379C>T | non_coding_transcript_exon_variant | 3/9 | 1 | ||||
TRIP13 | ENST00000513435.1 | c.252C>T | p.Ile84= | synonymous_variant | 3/8 | 5 | |||
TRIP13 | ENST00000508456.1 | n.233-40C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248642Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134332
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GnomAD4 exome AF: 0.0000880 AC: 128AN: 1454580Hom.: 0 Cov.: 31 AF XY: 0.0000789 AC XY: 57AN XY: 722426
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74332
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | This sequence change affects codon 88 of the TRIP13 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the TRIP13 protein. This variant is present in population databases (rs762063056, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with TRIP13-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at