rs28450766
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001039141.3(TRIOBP):c.4178C>T(p.Pro1393Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,606,316 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001039141.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIOBP | NM_001039141.3 | c.4178C>T | p.Pro1393Leu | missense_variant | 9/24 | ENST00000644935.1 | NP_001034230.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIOBP | ENST00000644935.1 | c.4178C>T | p.Pro1393Leu | missense_variant | 9/24 | NM_001039141.3 | ENSP00000496394.1 | |||
TRIOBP | ENST00000344404.10 | n.*3661C>T | non_coding_transcript_exon_variant | 7/22 | 2 | ENSP00000340312.6 | ||||
TRIOBP | ENST00000344404.10 | n.*3661C>T | 3_prime_UTR_variant | 7/22 | 2 | ENSP00000340312.6 |
Frequencies
GnomAD3 genomes AF: 0.00676 AC: 1029AN: 152110Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00162 AC: 373AN: 230630Hom.: 3 AF XY: 0.00124 AC XY: 157AN XY: 126340
GnomAD4 exome AF: 0.000754 AC: 1096AN: 1454088Hom.: 20 Cov.: 36 AF XY: 0.000627 AC XY: 453AN XY: 722802
GnomAD4 genome AF: 0.00681 AC: 1036AN: 152228Hom.: 13 Cov.: 32 AF XY: 0.00680 AC XY: 506AN XY: 74418
ClinVar
Submissions by phenotype
not specified Benign:3
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 | Apr 30, 2012 | Pro1393Leu in Exon 09 of TRIOBP: This variant is not expected to have clinical s ignificance because it has been identified in 1.7% (53/3054) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs28450766). - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 22, 2015 | - - |
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at