rs61742338
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000373327.5(TRAF3IP1):c.416G>A(p.Arg139Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,950 control chromosomes in the GnomAD database, including 1,053 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R139W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000373327.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.416G>A | p.Arg139Gln | missense_variant | 4/17 | ENST00000373327.5 | NP_056465.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.416G>A | p.Arg139Gln | missense_variant | 4/17 | 1 | NM_015650.4 | ENSP00000362424 | ||
TRAF3IP1 | ENST00000391993.7 | c.416G>A | p.Arg139Gln | missense_variant | 4/15 | 1 | ENSP00000375851 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.*285G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 3 | ENSP00000386648 |
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 3619AN: 151990Hom.: 59 Cov.: 32
GnomAD3 exomes AF: 0.0260 AC: 6525AN: 251372Hom.: 110 AF XY: 0.0265 AC XY: 3596AN XY: 135850
GnomAD4 exome AF: 0.0349 AC: 51046AN: 1461842Hom.: 995 Cov.: 31 AF XY: 0.0348 AC XY: 25284AN XY: 727226
GnomAD4 genome AF: 0.0238 AC: 3618AN: 152108Hom.: 58 Cov.: 32 AF XY: 0.0221 AC XY: 1646AN XY: 74342
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
TRAF3IP1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at