chr5-896429-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004237.4(TRIP13):c.259-236C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,204 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 86 hom., cov: 33)
Consequence
TRIP13
NM_004237.4 intron
NM_004237.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.09
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 5-896429-C-T is Benign according to our data. Variant chr5-896429-C-T is described in ClinVar as [Benign]. Clinvar id is 1272239.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.259-236C>T | intron_variant | ENST00000166345.8 | |||
TRIP13 | NM_001166260.2 | c.259-236C>T | intron_variant | ||||
TRIP13 | XM_011514163.2 | c.259-236C>T | intron_variant | ||||
TRIP13 | XM_047417879.1 | c.-201-236C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP13 | ENST00000166345.8 | c.259-236C>T | intron_variant | 1 | NM_004237.4 | P1 | |||
TRIP13 | ENST00000512024.5 | n.374-236C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
TRIP13 | ENST00000513435.1 | c.246-236C>T | intron_variant | 5 | |||||
TRIP13 | ENST00000508456.1 | n.233-281C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2775AN: 152086Hom.: 82 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0183 AC: 2787AN: 152204Hom.: 86 Cov.: 33 AF XY: 0.0178 AC XY: 1327AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 15, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at