rs567455701
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_145725.3(TRAF3):c.245+10_245+21del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,612,482 control chromosomes in the GnomAD database, including 18 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0054 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 8 hom. )
Consequence
TRAF3
NM_145725.3 splice_region, intron
NM_145725.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.744
Genes affected
TRAF3 (HGNC:12033): (TNF receptor associated factor 3) The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from, members of the TNF receptor (TNFR) superfamily. This protein participates in the signal transduction of CD40, a TNFR family member important for the activation of the immune response. This protein is found to be a critical component of the lymphotoxin-beta receptor (LTbetaR) signaling complex, which induces NF-kappaB activation and cell death initiated by LTbeta ligation. Epstein-Barr virus encoded latent infection membrane protein-1 (LMP1) can interact with this and several other members of the TRAF family, which may be essential for the oncogenic effects of LMP1. The protein also plays a role in the regulation of antiviral response. Mutations in this are associated with Encephalopathy, acute, infection-induced, herpes-specific 5. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 14-102870453-GCCCTCGCCCGGC-G is Benign according to our data. Variant chr14-102870453-GCCCTCGCCCGGC-G is described in ClinVar as [Benign]. Clinvar id is 473290.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00538 (820/152326) while in subpopulation AFR AF= 0.019 (788/41566). AF 95% confidence interval is 0.0179. There are 10 homozygotes in gnomad4. There are 377 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 820 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3 | NM_145725.3 | c.245+10_245+21del | splice_region_variant, intron_variant | ENST00000392745.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3 | ENST00000392745.8 | c.245+10_245+21del | splice_region_variant, intron_variant | 1 | NM_145725.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00537 AC: 818AN: 152208Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00142 AC: 349AN: 245754Hom.: 5 AF XY: 0.000929 AC XY: 124AN XY: 133438
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GnomAD4 exome AF: 0.000560 AC: 817AN: 1460156Hom.: 8 AF XY: 0.000465 AC XY: 338AN XY: 726356
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GnomAD4 genome ? AF: 0.00538 AC: 820AN: 152326Hom.: 10 Cov.: 32 AF XY: 0.00506 AC XY: 377AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Herpes simplex encephalitis, susceptibility to, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at