rs17854985
Positions:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015650.4(TRAF3IP1):āc.906T>Cā(p.Pro302Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 1,357,820 control chromosomes in the GnomAD database, including 4,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.12 ( 1753 hom., cov: 32)
Exomes š: 0.052 ( 2680 hom. )
Consequence
TRAF3IP1
NM_015650.4 synonymous
NM_015650.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.68
Genes affected
TRAF3IP1 (HGNC:17861): (TRAF3 interacting protein 1) The protein encoded by this gene interacts with TNF receptor-associated factor 3, tethering it to cytoskeletal microtubules. The encoded protein is also an inhibitor of the innate type I IFN response. Defects in this gene are a cause of Senior-Loken syndrome 9. [provided by RefSeq, Mar 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant 2-238329333-T-C is Benign according to our data. Variant chr2-238329333-T-C is described in ClinVar as [Benign]. Clinvar id is 1167551.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.68 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.906T>C | p.Pro302Pro | synonymous_variant | 5/17 | ENST00000373327.5 | NP_056465.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.906T>C | p.Pro302Pro | synonymous_variant | 5/17 | 1 | NM_015650.4 | ENSP00000362424.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.906T>C | p.Pro302Pro | synonymous_variant | 5/15 | 1 | ENSP00000375851.3 | |||
TRAF3IP1 | ENST00000409739.2 | n.*775T>C | non_coding_transcript_exon_variant | 5/5 | 3 | ENSP00000386648.2 | ||||
TRAF3IP1 | ENST00000409739.2 | n.*775T>C | 3_prime_UTR_variant | 5/5 | 3 | ENSP00000386648.2 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17696AN: 151986Hom.: 1748 Cov.: 32
GnomAD3 genomes
AF:
AC:
17696
AN:
151986
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0804 AC: 10662AN: 132600Hom.: 739 AF XY: 0.0752 AC XY: 5357AN XY: 71206
GnomAD3 exomes
AF:
AC:
10662
AN:
132600
Hom.:
AF XY:
AC XY:
5357
AN XY:
71206
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0516 AC: 62170AN: 1205716Hom.: 2680 Cov.: 32 AF XY: 0.0515 AC XY: 29862AN XY: 579336
GnomAD4 exome
AF:
AC:
62170
AN:
1205716
Hom.:
Cov.:
32
AF XY:
AC XY:
29862
AN XY:
579336
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.117 AC: 17728AN: 152104Hom.: 1753 Cov.: 32 AF XY: 0.119 AC XY: 8838AN XY: 74378
GnomAD4 genome
AF:
AC:
17728
AN:
152104
Hom.:
Cov.:
32
AF XY:
AC XY:
8838
AN XY:
74378
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
341
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
TRAF3IP1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at