rs34655947
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001039141.3(TRIOBP):c.5488-7del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 1,613,276 control chromosomes in the GnomAD database, including 2,803 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.060 ( 298 hom., cov: 31)
Exomes 𝑓: 0.057 ( 2505 hom. )
Consequence
TRIOBP
NM_001039141.3 splice_region, splice_polypyrimidine_tract, intron
NM_001039141.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.100
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 -16 ACMG points.
BP6
?
Variant 22-37755093-TG-T is Benign according to our data. Variant chr22-37755093-TG-T is described in ClinVar as [Benign]. Clinvar id is 43861.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0877 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIOBP | NM_001039141.3 | c.5488-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000644935.1 | |||
TRIOBP | NM_007032.5 | c.349-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TRIOBP | NM_138632.2 | c.349-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIOBP | ENST00000644935.1 | c.5488-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001039141.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0599 AC: 9119AN: 152144Hom.: 298 Cov.: 31
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GnomAD3 exomes AF: 0.0580 AC: 14445AN: 249054Hom.: 492 AF XY: 0.0541 AC XY: 7291AN XY: 134748
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GnomAD4 exome AF: 0.0567 AC: 82792AN: 1461014Hom.: 2505 Cov.: 32 AF XY: 0.0553 AC XY: 40195AN XY: 726764
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GnomAD4 genome ? AF: 0.0599 AC: 9124AN: 152262Hom.: 298 Cov.: 31 AF XY: 0.0600 AC XY: 4469AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 20, 2012 | 5488-7delG in intron 13 of TRIOBP: This variant is not expected to have clinical significance because it has been identified in 4.5% (97/2178) of chromosomes fr om a broad population (1000Genomes; dbSNP rs34655947) - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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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