rs3734553
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001270508.2(TNFAIP3):c.2117G>A(p.Arg706Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001270508.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFAIP3 | NM_001270508.2 | c.2117G>A | p.Arg706Gln | missense_variant | 9/9 | ENST00000612899.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFAIP3 | ENST00000612899.5 | c.2117G>A | p.Arg706Gln | missense_variant | 9/9 | 5 | NM_001270508.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151870Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249912Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135078
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460432Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726426
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151870Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74150
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on TNFAIP3 function (PMID: 20483768). 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: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1361196). This variant has not been reported in the literature in individuals affected with TNFAIP3-related conditions. This variant is present in population databases (rs3734553, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 706 of the TNFAIP3 protein (p.Arg706Gln). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at