6-111591329-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_147686.4(TRAF3IP2):āc.758C>Gā(p.Pro253Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,519,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_147686.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000212 AC: 38AN: 179478Hom.: 0 AF XY: 0.000244 AC XY: 23AN XY: 94334
GnomAD4 exome AF: 0.000170 AC: 233AN: 1367522Hom.: 0 Cov.: 30 AF XY: 0.000180 AC XY: 121AN XY: 670386
GnomAD4 genome AF: 0.000151 AC: 23AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74442
ClinVar
Submissions by phenotype
Candidiasis, familial, 8 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 18, 2022 | This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 253 of the TRAF3IP2 protein (p.Pro253Arg). This variant is present in population databases (rs146627823, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with TRAF3IP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 541098). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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