chr2-238320684-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015650.4(TRAF3IP1):c.22C>T(p.Arg8Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000212 in 1,413,744 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R8Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.22C>T | p.Arg8Trp | missense_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.22C>T | p.Arg8Trp | missense_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.22C>T | p.Arg8Trp | missense_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.22C>T | p.Arg8Trp | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000662 AC: 1AN: 151060Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000158 AC: 2AN: 1262684Hom.: 0 Cov.: 30 AF XY: 0.00000161 AC XY: 1AN XY: 622666
GnomAD4 genome ? AF: 0.00000662 AC: 1AN: 151060Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73750
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TRAF3IP1 protein function. ClinVar contains an entry for this variant (Variation ID: 966360). This variant has not been reported in the literature in individuals affected with TRAF3IP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 8 of the TRAF3IP1 protein (p.Arg8Trp). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at