chr2-238320563-GC-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_015650.4(TRAF3IP1):c.-99del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 980,564 control chromosomes in the GnomAD database, including 3,436 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.062 ( 395 hom., cov: 32)
Exomes 𝑓: 0.086 ( 3041 hom. )
Consequence
TRAF3IP1
NM_015650.4 5_prime_UTR
NM_015650.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.166
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 2-238320563-GC-G is Benign according to our data. Variant chr2-238320563-GC-G is described in ClinVar as [Benign]. Clinvar id is 1281208.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.-99del | 5_prime_UTR_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.-99del | 5_prime_UTR_variant | 1/17 | 1 | NM_015650.4 | |||
TRAF3IP1 | ENST00000391993.7 | c.-99del | 5_prime_UTR_variant | 1/15 | 1 | P1 | |||
TRAF3IP1 | ENST00000409739.2 | c.-99del | 5_prime_UTR_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0620 AC: 9340AN: 150644Hom.: 396 Cov.: 32
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GnomAD4 exome AF: 0.0857 AC: 71088AN: 829816Hom.: 3041 Cov.: 11 AF XY: 0.0865 AC XY: 33648AN XY: 389146
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at