NM_004239.4:c.790C>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4BP7
The NM_004239.4(TRIP11):c.790C>A(p.Arg264Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,611,734 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
TRIP11
NM_004239.4 synonymous
NM_004239.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.01
Publications
7 publications found
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]
TRIP11 Gene-Disease associations (from GenCC):
- achondrogenesis type IAInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet, G2P, Laboratory for Molecular Medicine
- TRIP11-related skeletal dysplasiaInheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.199).
BP7
Synonymous conserved (PhyloP=3.01 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004239.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRIP11 | NM_004239.4 | MANE Select | c.790C>A | p.Arg264Arg | synonymous | Exon 6 of 21 | NP_004230.2 | ||
| TRIP11 | NM_001321851.1 | c.787C>A | p.Arg263Arg | synonymous | Exon 6 of 21 | NP_001308780.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRIP11 | ENST00000267622.8 | TSL:1 MANE Select | c.790C>A | p.Arg264Arg | synonymous | Exon 6 of 21 | ENSP00000267622.4 | ||
| TRIP11 | ENST00000554357.5 | TSL:1 | c.22C>A | p.Arg8Arg | synonymous | Exon 1 of 15 | ENSP00000451032.1 | ||
| TRIP11 | ENST00000555516.6 | TSL:5 | c.*104C>A | downstream_gene | N/A | ENSP00000451944.1 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151924Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151924
Hom.:
Cov.:
32
Gnomad AFR
AF:
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Gnomad FIN
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000200 AC: 5AN: 250438 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
250438
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459810Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726154 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1459810
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
726154
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33376
American (AMR)
AF:
AC:
0
AN:
44514
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26072
East Asian (EAS)
AF:
AC:
3
AN:
39652
South Asian (SAS)
AF:
AC:
0
AN:
85752
European-Finnish (FIN)
AF:
AC:
0
AN:
53194
Middle Eastern (MID)
AF:
AC:
0
AN:
5644
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111306
Other (OTH)
AF:
AC:
0
AN:
60300
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.463
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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>80
Age
GnomAD4 genome 0.00000658 AC: 1AN: 151924Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74214 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151924
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74214
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41356
American (AMR)
AF:
AC:
0
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4812
European-Finnish (FIN)
AF:
AC:
0
AN:
10564
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67972
Other (OTH)
AF:
AC:
0
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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