5-893101-C-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004237.4(TRIP13):c.92+11C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,581,834 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 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
TRIP13
NM_004237.4 intron
NM_004237.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.81
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 -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 5-893101-C-A is Benign according to our data. Variant chr5-893101-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2819203.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.92+11C>A | intron_variant | Intron 1 of 12 | ENST00000166345.8 | NP_004228.1 | ||
TRIP13 | NM_001166260.2 | c.92+11C>A | intron_variant | Intron 1 of 8 | NP_001159732.1 | |||
TRIP13 | XM_011514163.2 | c.92+11C>A | intron_variant | Intron 1 of 13 | XP_011512465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.92+11C>A | intron_variant | Intron 1 of 12 | 1 | NM_004237.4 | ENSP00000166345.3 | |||
TRIP13 | ENST00000512024.5 | n.207+11C>A | intron_variant | Intron 1 of 8 | 1 | |||||
TRIP13 | ENST00000508456.1 | n.66+11C>A | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000467 AC: 9AN: 192746Hom.: 0 AF XY: 0.0000568 AC XY: 6AN XY: 105590
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GnomAD4 exome AF: 0.000115 AC: 164AN: 1429722Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 95AN XY: 709428
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74286
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
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