rs140528529
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001039141.3(TRIOBP):c.5588C>T(p.Ala1863Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,613,978 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 14 hom. )
Consequence
TRIOBP
NM_001039141.3 missense
NM_001039141.3 missense
Scores
11
7
Clinical Significance
Conservation
PhyloP100: 1.37
Genes affected
TRIOBP (HGNC:17009): (TRIO and F-actin binding protein) This gene encodes a protein with an N-terminal pleckstrin homology domain and a C-terminal coiled-coil region. The protein interacts with trio, which is involved with neural tissue development and controlling actin cytoskeleton organization, cell motility and cell growth. The protein also associates with F-actin and stabilizes F-actin structures. Mutations in this gene have been associated with a form of autosomal recessive nonsyndromic deafness. Multiple alternatively spliced transcript variants that would encode different isoforms have been found for this gene, however some transcripts may be subject to nonsense-mediated decay (NMD). [provided by RefSeq, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.013053089).
BP6
?
Variant 22-37755560-C-T is Benign according to our data. Variant chr22-37755560-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 177980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00192 (292/152332) while in subpopulation NFE AF= 0.00268 (182/68024). AF 95% confidence interval is 0.00236. There are 1 homozygotes in gnomad4. There are 164 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIOBP | NM_001039141.3 | c.5588C>T | p.Ala1863Val | missense_variant | 15/24 | ENST00000644935.1 | |
TRIOBP | NM_007032.5 | c.449C>T | p.Ala150Val | missense_variant | 5/14 | ||
TRIOBP | NM_138632.2 | c.449C>T | p.Ala150Val | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIOBP | ENST00000644935.1 | c.5588C>T | p.Ala1863Val | missense_variant | 15/24 | NM_001039141.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00192 AC: 292AN: 152214Hom.: 1 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00230 AC: 578AN: 251282Hom.: 5 AF XY: 0.00217 AC XY: 295AN XY: 135882
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GnomAD4 exome AF: 0.00225 AC: 3292AN: 1461646Hom.: 14 Cov.: 32 AF XY: 0.00226 AC XY: 1641AN XY: 727142
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GnomAD4 genome ? AF: 0.00192 AC: 292AN: 152332Hom.: 1 Cov.: 32 AF XY: 0.00220 AC XY: 164AN XY: 74486
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Uncertain:1Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | TRIOBP: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 02, 2019 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 19, 2015 | p.Ala1863Val in exon 15 of TRIOBP: This variant is not expected to have clinical significance because it has been identified in 0.33% (220/66206) of European ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs140528529). - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 03, 2017 | - - |
Meniere disease Uncertain:1
Uncertain significance, no assertion criteria provided | research | Center for Computational Biology & Bioinformatics, University of California, San Diego | Jun 03, 2024 | - - |
TRIOBP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T;T;.;.;.;D;T;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;L;.;.;.;.;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;D;D;.;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;.;D;D;.;D;D;D
Sift4G
Uncertain
D;.;D;D;.;D;D;D
Polyphen
D;D;.;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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