chr6-30198977-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The NM_003449.5(TRIM26):c.127G>A(p.Val43Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,612,528 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 (★).
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.127G>A | p.Val43Ile | missense_variant | 4/10 | ENST00000454678.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM26 | ENST00000454678.7 | c.127G>A | p.Val43Ile | missense_variant | 4/10 | 1 | NM_003449.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152064Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000114 AC: 28AN: 246276Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134262
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1460346Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 39AN XY: 726398
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 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