chr2-27305004-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_187841.3(TRIM54):c.559C>T(p.Arg187Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_187841.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM54 | ENST00000380075.7 | c.559C>T | p.Arg187Cys | missense_variant | Exon 4 of 9 | 1 | NM_187841.3 | ENSP00000369415.3 | ||
TRIM54 | ENST00000296098.4 | c.685C>T | p.Arg229Cys | missense_variant | Exon 5 of 10 | 1 | ENSP00000296098.4 | |||
TRIM54 | ENST00000488321.1 | n.314C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250864Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135714
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461816Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727218
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.685C>T (p.R229C) alteration is located in exon 5 (coding exon 5) of the TRIM54 gene. This alteration results from a C to T substitution at nucleotide position 685, causing the arginine (R) at amino acid position 229 to be replaced by a cysteine (C). 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