chr9-136920346-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_021138.4(TRAF2):c.791C>T(p.Ala264Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021138.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF2 | NM_021138.4 | c.791C>T | p.Ala264Val | missense_variant | 8/11 | ENST00000247668.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF2 | ENST00000247668.7 | c.791C>T | p.Ala264Val | missense_variant | 8/11 | 1 | NM_021138.4 | P1 | |
TRAF2 | ENST00000482854.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250840Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135806
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727172
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at