rs77981249
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004239.4(TRIP11):āc.405T>Cā(p.Ala135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.021 in 1,614,178 control chromosomes in the GnomAD database, including 730 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.019 ( 53 hom., cov: 32)
Exomes š: 0.021 ( 677 hom. )
Consequence
TRIP11
NM_004239.4 synonymous
NM_004239.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.216
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 14-92021739-A-G is Benign according to our data. Variant chr14-92021739-A-G is described in ClinVar as [Benign]. Clinvar id is 314977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.216 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP11 | NM_004239.4 | c.405T>C | p.Ala135= | synonymous_variant | 4/21 | ENST00000267622.8 | |
TRIP11 | NM_001321851.1 | c.402T>C | p.Ala134= | synonymous_variant | 4/21 | ||
TRIP11 | XR_001750598.3 | n.779T>C | non_coding_transcript_exon_variant | 4/15 | |||
TRIP11 | XR_943560.3 | n.779T>C | non_coding_transcript_exon_variant | 4/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP11 | ENST00000267622.8 | c.405T>C | p.Ala135= | synonymous_variant | 4/21 | 1 | NM_004239.4 | P1 | |
TRIP11 | ENST00000555516.6 | c.-79T>C | 5_prime_UTR_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0186 AC: 2834AN: 152194Hom.: 53 Cov.: 32
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GnomAD3 exomes AF: 0.0270 AC: 6775AN: 251354Hom.: 198 AF XY: 0.0289 AC XY: 3929AN XY: 135842
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GnomAD4 exome AF: 0.0213 AC: 31070AN: 1461866Hom.: 677 Cov.: 32 AF XY: 0.0225 AC XY: 16399AN XY: 727232
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GnomAD4 genome ? AF: 0.0186 AC: 2834AN: 152312Hom.: 53 Cov.: 32 AF XY: 0.0202 AC XY: 1507AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Achondrogenesis, type IA Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 26, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 28, 2023 | - - |
Connective tissue disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 11, 2021 | - - |
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