20-44051529-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098797.2(TOX2):c.635C>T(p.Ser212Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000682 in 1,598,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098797.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000331 AC: 8AN: 241394Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130176
GnomAD4 exome AF: 0.0000712 AC: 103AN: 1445884Hom.: 0 Cov.: 31 AF XY: 0.0000670 AC XY: 48AN XY: 716578
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.635C>T (p.S212L) alteration is located in exon 4 (coding exon 4) of the TOX2 gene. This alteration results from a C to T substitution at nucleotide position 635, causing the serine (S) at amino acid position 212 to be replaced by a leucine (L). 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