chr17-15642733-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001348119.1(TRIM16):c.603A>C(p.Gln201His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000925 in 864,802 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_001348119.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM16 | NM_001348119.1 | c.603A>C | p.Gln201His | missense_variant | 8/12 | ENST00000649191.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM16 | ENST00000649191.2 | c.603A>C | p.Gln201His | missense_variant | 8/12 | NM_001348119.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000481 AC: 6AN: 124710Hom.: 0 Cov.: 21
GnomAD3 exomes AF: 0.00000881 AC: 1AN: 113556Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60526
GnomAD4 exome AF: 0.00000270 AC: 2AN: 740092Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0AN XY: 380058
GnomAD4 genome ? AF: 0.0000481 AC: 6AN: 124710Hom.: 0 Cov.: 21 AF XY: 0.0000336 AC XY: 2AN XY: 59486
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 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