rs1491235
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134665.3(TRMT10A):c.*2366T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,904 control chromosomes in the GnomAD database, including 10,100 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 0.35 ( 10100 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
TRMT10A
NM_001134665.3 3_prime_UTR
NM_001134665.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Genes affected
TRMT10A (HGNC:28403): (tRNA methyltransferase 10A) This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT10A | NM_001134665.3 | c.*2366T>C | 3_prime_UTR_variant | 8/8 | ENST00000394876.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT10A | ENST00000394876.7 | c.*2366T>C | 3_prime_UTR_variant | 8/8 | 1 | NM_001134665.3 | P1 | ||
TRMT10A | ENST00000394877.7 | c.*2366T>C | 3_prime_UTR_variant | 8/8 | 2 | P1 | |||
TRMT10A | ENST00000273962.7 | downstream_gene_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.352 AC: 53476AN: 151786Hom.: 10069 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.353 AC: 53547AN: 151904Hom.: 10100 Cov.: 32 AF XY: 0.349 AC XY: 25923AN XY: 74240
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1389
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3470
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at