chr22-20115267-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_022727.6(TRMT2A):c.889C>T(p.Arg297Trp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000248 in 1,610,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022727.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT2A | NM_022727.6 | c.889C>T | p.Arg297Trp | missense_variant, splice_region_variant | 4/12 | ENST00000252136.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT2A | ENST00000252136.12 | c.889C>T | p.Arg297Trp | missense_variant, splice_region_variant | 4/12 | 1 | NM_022727.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248690Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134724
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458740Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 2AN XY: 725336
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.889C>T (p.R297W) alteration is located in exon 4 (coding exon 4) of the TRMT2A gene. This alteration results from a C to T substitution at nucleotide position 889, causing the arginine (R) at amino acid position 297 to be replaced by a tryptophan (W). 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