chr6-125986563-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001031712.3(TRMT11):c.13T>A(p.Cys5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000647 in 1,591,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031712.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT11 | NM_001031712.3 | c.13T>A | p.Cys5Ser | missense_variant | 1/13 | ENST00000334379.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT11 | ENST00000334379.11 | c.13T>A | p.Cys5Ser | missense_variant | 1/13 | 1 | NM_001031712.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000381 AC: 58AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000751 AC: 16AN: 213094Hom.: 0 AF XY: 0.0000524 AC XY: 6AN XY: 114574
GnomAD4 exome AF: 0.0000313 AC: 45AN: 1438958Hom.: 0 Cov.: 31 AF XY: 0.0000252 AC XY: 18AN XY: 713602
GnomAD4 genome ? AF: 0.000381 AC: 58AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.13T>A (p.C5S) alteration is located in exon 1 (coding exon 1) of the TRMT11 gene. This alteration results from a T to A substitution at nucleotide position 13, causing the cysteine (C) at amino acid position 5 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at