5-893099-G-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The NM_004237.4(TRIP13):c.92+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000253 in 1,581,774 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 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
TRIP13
NM_004237.4 intron
NM_004237.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0520
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 -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 5-893099-G-A is Benign according to our data. Variant chr5-893099-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3714393.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000394 (6/152200) while in subpopulation EAS AF= 0.000969 (5/5160). AF 95% confidence interval is 0.000381. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIP13 | NM_004237.4 | c.92+9G>A | intron_variant | Intron 1 of 12 | ENST00000166345.8 | NP_004228.1 | ||
TRIP13 | NM_001166260.2 | c.92+9G>A | intron_variant | Intron 1 of 8 | NP_001159732.1 | |||
TRIP13 | XM_011514163.2 | c.92+9G>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+9G>A | intron_variant | Intron 1 of 12 | 1 | NM_004237.4 | ENSP00000166345.3 | |||
TRIP13 | ENST00000512024.5 | n.207+9G>A | intron_variant | Intron 1 of 8 | 1 | |||||
TRIP13 | ENST00000508456.1 | n.66+9G>A | intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152082Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000832 AC: 16AN: 192328Hom.: 0 AF XY: 0.0000759 AC XY: 8AN XY: 105364
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GnomAD4 exome AF: 0.0000238 AC: 34AN: 1429574Hom.: 0 Cov.: 31 AF XY: 0.0000226 AC XY: 16AN XY: 709350
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74400
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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
Nov 30, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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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