chr2-238320685-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015650.4(TRAF3IP1):c.23G>A(p.Arg8Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000565 in 1,415,624 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. R8W) has been classified as Uncertain significance.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.23G>A | p.Arg8Gln | missense_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.23G>A | p.Arg8Gln | missense_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.23G>A | p.Arg8Gln | missense_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.23G>A | p.Arg8Gln | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151120Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000475 AC: 6AN: 1264396Hom.: 0 Cov.: 30 AF XY: 0.00000481 AC XY: 3AN XY: 623532
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151228Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73890
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2021 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TRAF3IP1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 8 of the TRAF3IP1 protein (p.Arg8Gln). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at