chr22-20116149-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022727.6(TRMT2A):c.488C>T(p.Pro163Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000818 in 1,612,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022727.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT2A | NM_022727.6 | c.488C>T | p.Pro163Leu | missense_variant | 2/12 | ENST00000252136.12 | |
RANBP1 | NM_001278639.2 | c.-36G>A | 5_prime_UTR_variant | 1/6 | ENST00000430524.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT2A | ENST00000252136.12 | c.488C>T | p.Pro163Leu | missense_variant | 2/12 | 1 | NM_022727.6 | P1 | |
RANBP1 | ENST00000430524.6 | c.-36G>A | 5_prime_UTR_variant | 1/6 | 3 | NM_001278639.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250248Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135560
GnomAD4 exome AF: 0.0000863 AC: 126AN: 1460678Hom.: 0 Cov.: 33 AF XY: 0.0000729 AC XY: 53AN XY: 726584
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.488C>T (p.P163L) alteration is located in exon 2 (coding exon 2) of the TRMT2A gene. This alteration results from a C to T substitution at nucleotide position 488, causing the proline (P) at amino acid position 163 to be replaced by a leucine (L). 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