chr2-238320750-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015650.4(TRAF3IP1):c.88C>T(p.Pro30Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000543 in 1,288,988 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P30L) has been classified as Uncertain significance.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.88C>T | p.Pro30Ser | missense_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.88C>T | p.Pro30Ser | missense_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.88C>T | p.Pro30Ser | missense_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.88C>T | p.Pro30Ser | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151338Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.0000404 AC: 4AN: 99046Hom.: 0 AF XY: 0.0000550 AC XY: 3AN XY: 54508
GnomAD4 exome AF: 0.00000543 AC: 7AN: 1288988Hom.: 0 Cov.: 33 AF XY: 0.00000786 AC XY: 5AN XY: 636044
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151338Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73906
ClinVar
Submissions by phenotype
Senior-Loken syndrome 9 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | DBGen Ocular Genomics | May 25, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 19, 2022 | This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 30 of the TRAF3IP1 protein (p.Pro30Ser). This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with TRAF3IP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 951276). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at