1-39883378-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_017646.6(TRIT1):c.114G>A(p.Thr38Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,126 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 (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
TRIT1
NM_017646.6 synonymous
NM_017646.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.822
Publications
0 publications found
Genes affected
TRIT1 (HGNC:20286): (tRNA isopentenyltransferase 1) This gene encodes a protein that that is targeted to the mitochondrion and modifies transfer RNAs (tRNAs) by adding a dimethylallyl group onto the adenine at position 37. This modification is important for maintaining the correct reading frame during protein translation. This gene is considered a tumor suppressor and its expression can decrease cell growth. Alternative splicing results in multiple transcripts variants, most of which are likely non-functional. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 1-39883378-C-T is Benign according to our data. Variant chr1-39883378-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3058604.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.822 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_017646.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRIT1 | NM_017646.6 | MANE Select | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 11 | NP_060116.2 | ||
| TRIT1 | NM_001312691.1 | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 10 | NP_001299620.1 | Q9H3H1-4 | ||
| TRIT1 | NM_001312692.1 | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 9 | NP_001299621.1 | Q9H3H1-5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRIT1 | ENST00000316891.10 | TSL:1 MANE Select | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 11 | ENSP00000321810.5 | Q9H3H1-1 | |
| TRIT1 | ENST00000372818.5 | TSL:1 | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 10 | ENSP00000361905.1 | Q9H3H1-4 | |
| TRIT1 | ENST00000441669.6 | TSL:1 | c.114G>A | p.Thr38Thr | synonymous | Exon 1 of 9 | ENSP00000388333.2 | Q9H3H1-5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461126Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726850 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461126
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
726850
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33466
American (AMR)
AF:
AC:
0
AN:
44654
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26100
East Asian (EAS)
AF:
AC:
0
AN:
39684
South Asian (SAS)
AF:
AC:
0
AN:
86160
European-Finnish (FIN)
AF:
AC:
0
AN:
53294
Middle Eastern (MID)
AF:
AC:
0
AN:
5642
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111806
Other (OTH)
AF:
AC:
0
AN:
60320
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
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10
<30
30-35
35-40
40-45
45-50
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55-60
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
1
TRIT1-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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