chr2-238320752-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015650.4(TRAF3IP1):c.90C>G(p.Pro30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000416 in 1,440,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000023 ( 0 hom. )
Consequence
TRAF3IP1
NM_015650.4 synonymous
NM_015650.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.417
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
Variant 2-238320752-C-G is Benign according to our data. Variant chr2-238320752-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1934652.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.417 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.90C>G | p.Pro30= | synonymous_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.90C>G | p.Pro30= | synonymous_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.90C>G | p.Pro30= | synonymous_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.90C>G | p.Pro30= | synonymous_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151356Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000233 AC: 3AN: 1289302Hom.: 0 Cov.: 33 AF XY: 0.00000472 AC XY: 3AN XY: 636170
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at