5-14143778-C-CCGCGGCGGCCAG
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The ENST00000344204.9(TRIO):c.60_71dup(p.Ala21_Ala24dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Consequence
TRIO
ENST00000344204.9 inframe_insertion
ENST00000344204.9 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.960
Genes affected
TRIO (HGNC:12303): (trio Rho guanine nucleotide exchange factor) This gene encodes a large protein that functions as a GDP to GTP exchange factor. This protein promotes the reorganization of the actin cytoskeleton, thereby playing a role in cell migration and growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in ENST00000344204.9.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIO | NM_007118.4 | c.60_71dup | p.Ala21_Ala24dup | inframe_insertion | 1/57 | ENST00000344204.9 | NP_009049.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIO | ENST00000344204.9 | c.60_71dup | p.Ala21_Ala24dup | inframe_insertion | 1/57 | 1 | NM_007118.4 | ENSP00000339299 | P1 | |
TRIO | ENST00000698541.1 | c.60_71dup | p.Ala21_Ala24dup | inframe_insertion | 1/37 | ENSP00000513786 | ||||
TRIO | ENST00000502816.1 | n.84_95dup | non_coding_transcript_exon_variant | 1/5 | 2 | |||||
TRIO | ENST00000505971.5 | n.84_95dup | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 25, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In-frame duplication of 4 amino acids in a non-repeat region; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.