11-89798233-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020358.2(TRIM49):c.1256C>A(p.Thr419Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000262 in 1,566,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM49 | NM_020358.2 | c.1256C>A | p.Thr419Asn | missense_variant | 8/8 | ENST00000329758.5 | |
TRIM49 | XM_017018027.3 | c.1025C>A | p.Thr342Asn | missense_variant | 5/5 | ||
TRIM49 | XM_024448617.2 | c.738+3469C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM49 | ENST00000329758.5 | c.1256C>A | p.Thr419Asn | missense_variant | 8/8 | 1 | NM_020358.2 | A2 | |
TRIM49 | ENST00000532501.2 | c.1025C>A | p.Thr342Asn | missense_variant | 6/6 | 5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000326 AC: 4AN: 122552Hom.: 0 Cov.: 17
GnomAD3 exomes AF: 0.0000343 AC: 8AN: 233148Hom.: 0 AF XY: 0.0000315 AC XY: 4AN XY: 127072
GnomAD4 exome AF: 0.0000256 AC: 37AN: 1443990Hom.: 0 Cov.: 30 AF XY: 0.0000362 AC XY: 26AN XY: 718242
GnomAD4 genome AF: 0.0000326 AC: 4AN: 122634Hom.: 0 Cov.: 17 AF XY: 0.0000170 AC XY: 1AN XY: 58734
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.1256C>A (p.T419N) alteration is located in exon 8 (coding exon 6) of the TRIM49 gene. This alteration results from a C to A substitution at nucleotide position 1256, causing the threonine (T) at amino acid position 419 to be replaced by an asparagine (N). 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