16-52439314-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001080430.4(TOX3):c.1642G>A(p.Gly548Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000171 in 1,461,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080430.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TOX3 | ENST00000219746.14 | c.1642G>A | p.Gly548Arg | missense_variant | Exon 7 of 7 | 2 | NM_001080430.4 | ENSP00000219746.9 | ||
TOX3 | ENST00000407228.7 | c.1627G>A | p.Gly543Arg | missense_variant | Exon 8 of 8 | 2 | ENSP00000385705.3 | |||
TOX3 | ENST00000566696.1 | n.2106G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248854Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135018
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461388Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726974
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1642G>A (p.G548R) alteration is located in exon 7 (coding exon 7) of the TOX3 gene. This alteration results from a G to A substitution at nucleotide position 1642, causing the glycine (G) at amino acid position 548 to be replaced by an arginine (R). 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