6-30196719-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The NM_003449.5(TRIM26):c.562A>G(p.Ile188Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,614,228 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I188T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003449.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM26 | NM_003449.5 | c.562A>G | p.Ile188Val | missense_variant | 6/10 | ENST00000454678.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM26 | ENST00000454678.7 | c.562A>G | p.Ile188Val | missense_variant | 6/10 | 1 | NM_003449.5 | P1 | |
TRIM26 | ENST00000437089.5 | c.562A>G | p.Ile188Val | missense_variant | 5/9 | 1 | P1 | ||
TRIM26 | ENST00000453195.5 | c.562A>G | p.Ile188Val | missense_variant | 5/9 | 1 | P1 | ||
TRIM26 | ENST00000416596.5 | c.562A>G | p.Ile188Val | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250546Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135608
GnomAD4 exome AF: 0.0000711 AC: 104AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.0000756 AC XY: 55AN XY: 727242
GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74510
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at