chr1-155175986-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_025058.5(TRIM46):c.424C>T(p.Arg142Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R142Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_025058.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM46 | ENST00000334634.9 | c.424C>T | p.Arg142Trp | missense_variant | Exon 3 of 10 | 1 | NM_025058.5 | ENSP00000334657.4 | ||
ENSG00000273088 | ENST00000473363.3 | c.49-2512G>A | intron_variant | Intron 1 of 4 | 5 | ENSP00000477381.3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 250632Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135420
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461150Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 726758
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.424C>T (p.R142W) alteration is located in exon 3 (coding exon 3) of the TRIM46 gene. This alteration results from a C to T substitution at nucleotide position 424, causing the arginine (R) at amino acid position 142 to be replaced by a tryptophan (W). 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