chr14-60975180-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_020810.3(TRMT5):c.1459C>T(p.Pro487Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000441 in 1,605,578 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P487P) has been classified as Benign.
Frequency
Consequence
NM_020810.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT5 | NM_020810.3 | c.1459C>T | p.Pro487Ser | missense_variant | 5/5 | ENST00000261249.7 | |
TRMT5 | NM_001350253.1 | c.1543C>T | p.Pro515Ser | missense_variant | 5/5 | ||
TRMT5 | NM_001350254.1 | c.1540C>T | p.Pro514Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT5 | ENST00000261249.7 | c.1459C>T | p.Pro487Ser | missense_variant | 5/5 | 1 | NM_020810.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000428 AC: 105AN: 245342Hom.: 0 AF XY: 0.000436 AC XY: 58AN XY: 132894
GnomAD4 exome AF: 0.000448 AC: 651AN: 1453394Hom.: 1 Cov.: 30 AF XY: 0.000433 AC XY: 313AN XY: 722926
GnomAD4 genome AF: 0.000375 AC: 57AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74402
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.1459C>T (p.P487S) alteration is located in exon 5 (coding exon 5) of the TRMT5 gene. This alteration results from a C to T substitution at nucleotide position 1459, causing the proline (P) at amino acid position 487 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at