chr5-900528-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004237.4(TRIP13):c.423C>T(p.Tyr141=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,611,556 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
TRIP13
NM_004237.4 synonymous
NM_004237.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0190
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 -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 5-900528-C-T is Benign according to our data. Variant chr5-900528-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3061491.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.019 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.423C>T | p.Tyr141= | synonymous_variant | 4/13 | ENST00000166345.8 | |
TRIP13 | NM_001166260.2 | c.423C>T | p.Tyr141= | synonymous_variant | 4/9 | ||
TRIP13 | XM_011514163.2 | c.423C>T | p.Tyr141= | synonymous_variant | 4/14 | ||
TRIP13 | XM_047417879.1 | c.-37C>T | 5_prime_UTR_variant | 4/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.423C>T | p.Tyr141= | synonymous_variant | 4/13 | 1 | NM_004237.4 | P1 | |
TRIP13 | ENST00000512024.5 | n.538C>T | non_coding_transcript_exon_variant | 4/9 | 1 | ||||
TRIP13 | ENST00000513435.1 | c.411C>T | p.Tyr137= | synonymous_variant | 4/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248230Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134202
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GnomAD4 exome AF: 0.0000206 AC: 30AN: 1459298Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 725958
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74438
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TRIP13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 17, 2021 | 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). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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