chr16-52439418-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001080430.4(TOX3):c.1538G>A(p.Arg513His) variant causes a missense change. The variant allele was found at a frequency of 0.0000469 in 1,555,158 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R513C) has been classified as Benign.
Frequency
Consequence
NM_001080430.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOX3 | NM_001080430.4 | c.1538G>A | p.Arg513His | missense_variant | 7/7 | ENST00000219746.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOX3 | ENST00000219746.14 | c.1538G>A | p.Arg513His | missense_variant | 7/7 | 2 | NM_001080430.4 | A2 | |
TOX3 | ENST00000407228.7 | c.1523G>A | p.Arg508His | missense_variant | 8/8 | 2 | P2 | ||
TOX3 | ENST00000566696.1 | n.2002G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000593 AC: 9AN: 151798Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000383 AC: 7AN: 182588Hom.: 0 AF XY: 0.0000306 AC XY: 3AN XY: 97934
GnomAD4 exome AF: 0.0000456 AC: 64AN: 1403360Hom.: 0 Cov.: 30 AF XY: 0.0000474 AC XY: 33AN XY: 695652
GnomAD4 genome ? AF: 0.0000593 AC: 9AN: 151798Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74120
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | 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