9-136898904-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_021138.4(TRAF2):c.164C>T(p.Ser55Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,610,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021138.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAF2 | NM_021138.4 | c.164C>T | p.Ser55Phe | missense_variant | Exon 2 of 11 | ENST00000247668.7 | NP_066961.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAF2 | ENST00000247668.7 | c.164C>T | p.Ser55Phe | missense_variant | Exon 2 of 11 | 1 | NM_021138.4 | ENSP00000247668.2 | ||
TRAF2 | ENST00000429509.5 | c.164C>T | p.Ser55Phe | missense_variant | Exon 2 of 6 | 3 | ENSP00000406524.1 | |||
TRAF2 | ENST00000419057.5 | c.164C>T | p.Ser55Phe | missense_variant | Exon 3 of 6 | 3 | ENSP00000405860.1 | |||
TRAF2 | ENST00000414589.1 | c.164C>T | p.Ser55Phe | missense_variant | Exon 4 of 6 | 3 | ENSP00000397653.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243834Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132504
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1458432Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 6AN XY: 725398
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164C>T (p.S55F) alteration is located in exon 2 (coding exon 1) of the TRAF2 gene. This alteration results from a C to T substitution at nucleotide position 164, causing the serine (S) at amino acid position 55 to be replaced by a phenylalanine (F). 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