rs2235978
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004239.4(TRIP11):c.139+1623G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,980 control chromosomes in the GnomAD database, including 6,722 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.29 ( 6722 hom., cov: 32)
Consequence
TRIP11
NM_004239.4 intron
NM_004239.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.536
Genes affected
TRIP11 (HGNC:12305): (thyroid hormone receptor interactor 11) This gene was identified based on the interaction of its protein product with thyroid hormone receptor beta. This protein is associated with the Golgi apparatus. The N-terminal region of the protein binds Golgi membranes and the C-terminal region binds the minus ends of microtubules; thus, the protein is thought to play a role in assembly and maintenance of the Golgi ribbon structure around the centrosome. Mutations in this gene cause achondrogenesis type IA.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP11 | NM_004239.4 | c.139+1623G>T | intron_variant | ENST00000267622.8 | |||
TRIP11 | NM_001321851.1 | c.139+1623G>T | intron_variant | ||||
TRIP11 | XR_001750598.3 | n.513+1623G>T | intron_variant, non_coding_transcript_variant | ||||
TRIP11 | XR_943560.3 | n.513+1623G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP11 | ENST00000267622.8 | c.139+1623G>T | intron_variant | 1 | NM_004239.4 | P1 | |||
TRIP11 | ENST00000555105.1 | n.471+1623G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
TRIP11 | ENST00000555516.6 | c.-345+2956G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.288 AC: 43697AN: 151862Hom.: 6702 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.288 AC: 43750AN: 151980Hom.: 6722 Cov.: 32 AF XY: 0.287 AC XY: 21303AN XY: 74298
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74298
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1276
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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