1-209781373-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025228.4(TRAF3IP3):c.1478A>G(p.Asn493Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,461,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025228.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP3 | NM_025228.4 | c.1478A>G | p.Asn493Ser | missense_variant | 16/17 | ENST00000367025.8 | |
C1orf74 | NM_152485.4 | c.*1452T>C | 3_prime_UTR_variant | 2/2 | ENST00000294811.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP3 | ENST00000367025.8 | c.1478A>G | p.Asn493Ser | missense_variant | 16/17 | 1 | NM_025228.4 | P1 | |
C1orf74 | ENST00000294811.2 | c.*1452T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_152485.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251402Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135862
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461030Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726846
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.1478A>G (p.N493S) alteration is located in exon 16 (coding exon 14) of the TRAF3IP3 gene. This alteration results from a A to G substitution at nucleotide position 1478, causing the asparagine (N) at amino acid position 493 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at