NM_187841.3:c.159C>T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1
The NM_187841.3(TRIM54):c.159C>T(p.Asp53Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 1,611,688 control chromosomes in the GnomAD database, including 3,006 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_187841.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM54 | ENST00000380075.7 | c.159C>T | p.Asp53Asp | synonymous_variant | Exon 1 of 9 | 1 | NM_187841.3 | ENSP00000369415.3 | ||
TRIM54 | ENST00000296098.4 | c.159C>T | p.Asp53Asp | synonymous_variant | Exon 1 of 10 | 1 | ENSP00000296098.4 |
Frequencies
GnomAD3 genomes AF: 0.0458 AC: 6973AN: 152224Hom.: 225 Cov.: 32
GnomAD3 exomes AF: 0.0457 AC: 11324AN: 247974Hom.: 421 AF XY: 0.0455 AC XY: 6097AN XY: 133906
GnomAD4 exome AF: 0.0573 AC: 83653AN: 1459346Hom.: 2783 Cov.: 30 AF XY: 0.0561 AC XY: 40748AN XY: 725868
GnomAD4 genome AF: 0.0458 AC: 6971AN: 152342Hom.: 223 Cov.: 32 AF XY: 0.0453 AC XY: 3375AN XY: 74502
ClinVar
Submissions by phenotype
TRIM54-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at