chr14-91969063-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004239.4(TRIP11):c.*610A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00933 in 222,812 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 40 hom., cov: 32)
Exomes 𝑓: 0.0031 ( 9 hom. )
Consequence
TRIP11
NM_004239.4 3_prime_UTR
NM_004239.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.732
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 14-91969063-T-G is Benign according to our data. Variant chr14-91969063-T-G is described in ClinVar as [Benign]. Clinvar id is 314908.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1861/152164) while in subpopulation AFR AF= 0.0409 (1697/41480). AF 95% confidence interval is 0.0393. There are 40 homozygotes in gnomad4. There are 871 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 40 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP11 | NM_004239.4 | c.*610A>C | 3_prime_UTR_variant | 21/21 | ENST00000267622.8 | ||
TRIP11 | NM_001321851.1 | c.*610A>C | 3_prime_UTR_variant | 21/21 | |||
TRIP11 | XM_047431935.1 | c.*610A>C | 3_prime_UTR_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP11 | ENST00000267622.8 | c.*610A>C | 3_prime_UTR_variant | 21/21 | 1 | NM_004239.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0123 AC: 1863AN: 152046Hom.: 40 Cov.: 32
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GnomAD4 exome AF: 0.00307 AC: 217AN: 70648Hom.: 9 Cov.: 0 AF XY: 0.00286 AC XY: 94AN XY: 32858
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Achondrogenesis, type IA Benign:1
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. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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