2-238320763-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_015650.4(TRAF3IP1):c.101A>G(p.Tyr34Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000021 in 1,427,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Y34Y) has been classified as Likely benign.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.101A>G | p.Tyr34Cys | missense_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.101A>G | p.Tyr34Cys | missense_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.101A>G | p.Tyr34Cys | missense_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.101A>G | p.Tyr34Cys | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000662 AC: 1AN: 151158Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000157 AC: 2AN: 1276834Hom.: 0 Cov.: 33 AF XY: 0.00000317 AC XY: 2AN XY: 629944
GnomAD4 genome ? AF: 0.00000662 AC: 1AN: 151158Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73808
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 04, 2022 | This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 34 of the TRAF3IP1 protein (p.Tyr34Cys). 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 variant has not been reported in the literature in individuals affected with TRAF3IP1-related conditions. 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 disruptive. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at