2-27299425-CAG-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_187841.3(TRIM54):c.513+10_513+11delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000742 in 1,612,932 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_187841.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM54 | ENST00000380075.7 | c.513+10_513+11delAG | intron_variant | Intron 3 of 8 | 1 | NM_187841.3 | ENSP00000369415.3 | |||
TRIM54 | ENST00000296098.4 | c.513+10_513+11delAG | intron_variant | Intron 3 of 9 | 1 | ENSP00000296098.4 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000511 AC: 127AN: 248768Hom.: 0 AF XY: 0.000431 AC XY: 58AN XY: 134562
GnomAD4 exome AF: 0.000739 AC: 1080AN: 1460660Hom.: 1 AF XY: 0.000690 AC XY: 501AN XY: 726594
GnomAD4 genome AF: 0.000768 AC: 117AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74456
ClinVar
Submissions by phenotype
TRIM54-related disorder Benign:1
This variant is classified as likely 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