chr9-120926000-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005658.5(TRAF1):c.76G>A(p.Val26Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,096 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 Uncertain significance (★).
Frequency
Consequence
NM_005658.5 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 |
---|---|---|---|---|---|---|---|
TRAF1 | NM_005658.5 | c.76G>A | p.Val26Ile | missense_variant | 2/8 | ENST00000373887.8 | |
TRAF1 | NM_001190945.2 | c.76G>A | p.Val26Ile | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF1 | ENST00000373887.8 | c.76G>A | p.Val26Ile | missense_variant | 2/8 | 1 | NM_005658.5 | P1 | |
TRAF1 | ENST00000540010.1 | c.76G>A | p.Val26Ile | missense_variant | 3/9 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249810Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135096
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460880Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726768
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2023 | The c.76G>A (p.V26I) alteration is located in exon 2 (coding exon 1) of the TRAF1 gene. This alteration results from a G to A substitution at nucleotide position 76, causing the valine (V) at amino acid position 26 to be replaced by an isoleucine (I). 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