11-89798404-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020358.2(TRIM49):c.1085G>A(p.Arg362Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000518 in 1,603,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020358.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM49 | NM_020358.2 | c.1085G>A | p.Arg362Gln | missense_variant | Exon 8 of 8 | ENST00000329758.5 | NP_065091.1 | |
TRIM49 | XM_017018027.3 | c.854G>A | p.Arg285Gln | missense_variant | Exon 5 of 5 | XP_016873516.1 | ||
TRIM49 | XM_024448617.2 | c.738+3298G>A | intron_variant | Intron 3 of 5 | XP_024304385.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000160 AC: 23AN: 143610Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.000163 AC: 41AN: 250900Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135650
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1459368Hom.: 0 Cov.: 63 AF XY: 0.0000427 AC XY: 31AN XY: 726040
GnomAD4 genome AF: 0.000174 AC: 25AN: 143714Hom.: 0 Cov.: 23 AF XY: 0.000200 AC XY: 14AN XY: 69976
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1085G>A (p.R362Q) alteration is located in exon 8 (coding exon 6) of the TRIM49 gene. This alteration results from a G to A substitution at nucleotide position 1085, causing the arginine (R) at amino acid position 362 to be replaced by a glutamine (Q). 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