chr6-30196718-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_003449.5(TRIM26):c.563T>C(p.Ile188Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,614,180 control chromosomes in the GnomAD database, including 1 homozygotes. 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. I188V) has been classified as Likely benign.
Frequency
Consequence
NM_003449.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM26 | NM_003449.5 | c.563T>C | p.Ile188Thr | missense_variant | 6/10 | ENST00000454678.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM26 | ENST00000454678.7 | c.563T>C | p.Ile188Thr | missense_variant | 6/10 | 1 | NM_003449.5 | P1 | |
TRIM26 | ENST00000437089.5 | c.563T>C | p.Ile188Thr | missense_variant | 5/9 | 1 | P1 | ||
TRIM26 | ENST00000453195.5 | c.563T>C | p.Ile188Thr | missense_variant | 5/9 | 1 | P1 | ||
TRIM26 | ENST00000416596.5 | c.563T>C | p.Ile188Thr | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 250604Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135636
GnomAD4 exome AF: 0.000126 AC: 184AN: 1461880Hom.: 1 Cov.: 33 AF XY: 0.000183 AC XY: 133AN XY: 727240
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2023 | The c.563T>C (p.I188T) alteration is located in exon 6 (coding exon 3) of the TRIM26 gene. This alteration results from a T to C substitution at nucleotide position 563, causing the isoleucine (I) at amino acid position 188 to be replaced by a threonine (T). 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