9-136898748-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021138.4(TRAF2):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF2 | NM_021138.4 | c.8C>T | p.Ala3Val | missense_variant | 2/11 | ENST00000247668.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF2 | ENST00000247668.7 | c.8C>T | p.Ala3Val | missense_variant | 2/11 | 1 | NM_021138.4 | P1 | |
TRAF2 | ENST00000429509.5 | c.8C>T | p.Ala3Val | missense_variant | 2/6 | 3 | |||
TRAF2 | ENST00000419057.5 | c.8C>T | p.Ala3Val | missense_variant | 3/6 | 3 | |||
TRAF2 | ENST00000414589.1 | c.8C>T | p.Ala3Val | missense_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250302Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135572
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461060Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 726856
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.8C>T (p.A3V) 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 8, causing the alanine (A) at amino acid position 3 to be replaced by a valine (V). 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