X-140503897-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005634.3(SOX3):c.1164C>T(p.His388His) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000373 in 1,073,561 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005634.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 111816Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34100 FAILED QC
GnomAD3 exomes AF: 0.0000141 AC: 2AN: 142022Hom.: 0 AF XY: 0.0000207 AC XY: 1AN XY: 48300
GnomAD4 exome AF: 0.00000373 AC: 4AN: 1073561Hom.: 0 Cov.: 32 AF XY: 0.00000284 AC XY: 1AN XY: 351561
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 111816Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34100
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change affects codon 388 of the SOX3 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SOX3 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SOX3-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at