rs41288823
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_187841.3(TRIM54):c.662G>A(p.Cys221Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000649 in 1,613,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM54 | ENST00000380075.7 | c.662G>A | p.Cys221Tyr | missense_variant | Exon 5 of 9 | 1 | NM_187841.3 | ENSP00000369415.3 | ||
TRIM54 | ENST00000296098.4 | c.788G>A | p.Cys263Tyr | missense_variant | Exon 6 of 10 | 1 | ENSP00000296098.4 | |||
TRIM54 | ENST00000485306.1 | n.452G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
TRIM54 | ENST00000488321.1 | n.417G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000420 AC: 64AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000606 AC: 151AN: 249188Hom.: 0 AF XY: 0.000533 AC XY: 72AN XY: 134958
GnomAD4 exome AF: 0.000673 AC: 984AN: 1461438Hom.: 0 Cov.: 31 AF XY: 0.000604 AC XY: 439AN XY: 727026
GnomAD4 genome AF: 0.000420 AC: 64AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.788G>A (p.C263Y) alteration is located in exon 6 (coding exon 6) of the TRIM54 gene. This alteration results from a G to A substitution at nucleotide position 788, causing the cysteine (C) at amino acid position 263 to be replaced by a tyrosine (Y). 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