rs230310

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017646.6(TRIT1):​c.1235-134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 957,182 control chromosomes in the GnomAD database, including 288,736 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.81 ( 50608 hom., cov: 33)
Exomes 𝑓: 0.77 ( 238128 hom. )

Consequence

TRIT1
NM_017646.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293
Variant links:
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIT1NM_017646.6 linkuse as main transcriptc.1235-134T>C intron_variant ENST00000316891.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIT1ENST00000316891.10 linkuse as main transcriptc.1235-134T>C intron_variant 1 NM_017646.6 P1Q9H3H1-1

Frequencies

GnomAD3 genomes
AF:
0.810
AC:
123213
AN:
152122
Hom.:
50558
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.947
Gnomad AMI
AF:
0.796
Gnomad AMR
AF:
0.693
Gnomad ASJ
AF:
0.890
Gnomad EAS
AF:
0.679
Gnomad SAS
AF:
0.757
Gnomad FIN
AF:
0.782
Gnomad MID
AF:
0.799
Gnomad NFE
AF:
0.768
Gnomad OTH
AF:
0.782
GnomAD4 exome
AF:
0.767
AC:
617572
AN:
804940
Hom.:
238128
AF XY:
0.767
AC XY:
312641
AN XY:
407506
show subpopulations
Gnomad4 AFR exome
AF:
0.951
Gnomad4 AMR exome
AF:
0.664
Gnomad4 ASJ exome
AF:
0.882
Gnomad4 EAS exome
AF:
0.710
Gnomad4 SAS exome
AF:
0.755
Gnomad4 FIN exome
AF:
0.788
Gnomad4 NFE exome
AF:
0.764
Gnomad4 OTH exome
AF:
0.777
GnomAD4 genome
AF:
0.810
AC:
123318
AN:
152242
Hom.:
50608
Cov.:
33
AF XY:
0.807
AC XY:
60067
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.947
Gnomad4 AMR
AF:
0.693
Gnomad4 ASJ
AF:
0.890
Gnomad4 EAS
AF:
0.679
Gnomad4 SAS
AF:
0.758
Gnomad4 FIN
AF:
0.782
Gnomad4 NFE
AF:
0.768
Gnomad4 OTH
AF:
0.777
Alfa
AF:
0.771
Hom.:
61582
Bravo
AF:
0.809
Asia WGS
AF:
0.757
AC:
2633
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.7
DANN
Benign
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs230310; hg19: chr1-40307719; API