5-14143845-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007118.4(TRIO):c.120C>T(p.Ala40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000675 in 148,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 31)
Consequence
TRIO
NM_007118.4 synonymous
NM_007118.4 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.60
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 5-14143845-C-T is Benign according to our data. Variant chr5-14143845-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2655301.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.6 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIO | NM_007118.4 | c.120C>T | p.Ala40= | synonymous_variant | 1/57 | ENST00000344204.9 | NP_009049.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIO | ENST00000344204.9 | c.120C>T | p.Ala40= | synonymous_variant | 1/57 | 1 | NM_007118.4 | ENSP00000339299 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000675 AC: 1AN: 148150Hom.: 0 Cov.: 31
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GnomAD4 exome Cov.: 30
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GnomAD4 genome AF: 0.00000675 AC: 1AN: 148150Hom.: 0 Cov.: 31 AF XY: 0.0000139 AC XY: 1AN XY: 72182
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | TRIO: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at