9-97904896-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016481.5(TRMO):c.1163G>T(p.Arg388Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R388H) has been classified as Uncertain significance.
Frequency
Consequence
NM_016481.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMO | NM_016481.5 | c.1163G>T | p.Arg388Leu | missense_variant | 5/5 | ENST00000375119.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMO | ENST00000375119.8 | c.1163G>T | p.Arg388Leu | missense_variant | 5/5 | 1 | NM_016481.5 | P1 | |
TRMO | ENST00000375118.1 | c.725G>T | p.Arg242Leu | missense_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251460Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.1163G>T (p.R388L) alteration is located in exon 5 (coding exon 5) of the TRMO gene. This alteration results from a G to T substitution at nucleotide position 1163, causing the arginine (R) at amino acid position 388 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