6-25971899-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006355.5(TRIM38):c.538C>T(p.Arg180Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006355.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM38 | NM_006355.5 | c.538C>T | p.Arg180Trp | missense_variant | Exon 5 of 8 | ENST00000357085.5 | NP_006346.1 | |
TRIM38 | XM_047418080.1 | c.538C>T | p.Arg180Trp | missense_variant | Exon 5 of 9 | XP_047274036.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251154Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135732
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727224
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.538C>T (p.R180W) alteration is located in exon 5 (coding exon 3) of the TRIM38 gene. This alteration results from a C to T substitution at nucleotide position 538, causing the arginine (R) at amino acid position 180 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