X-101020552-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_024917.6(TRMT2B):c.1103G>A(p.Arg368Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000579 in 1,209,350 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024917.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRMT2B | NM_024917.6 | c.1103G>A | p.Arg368Gln | missense_variant | Exon 11 of 14 | ENST00000372936.4 | NP_079193.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRMT2B | ENST00000372936.4 | c.1103G>A | p.Arg368Gln | missense_variant | Exon 11 of 14 | 1 | NM_024917.6 | ENSP00000362027.3 | ||
TRMT2B | ENST00000372935.5 | c.1103G>A | p.Arg368Gln | missense_variant | Exon 11 of 14 | 1 | ENSP00000362026.1 | |||
TRMT2B | ENST00000545398.5 | c.1103G>A | p.Arg368Gln | missense_variant | Exon 10 of 13 | 1 | ENSP00000438134.1 | |||
TRMT2B | ENST00000372939.5 | c.968G>A | p.Arg323Gln | missense_variant | Exon 11 of 14 | 1 | ENSP00000362030.1 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112122Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34292
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097228Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 362602
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112122Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34292
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at