X-140503818-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005634.3(SOX3):c.1243G>A(p.Ala415Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,176,717 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005634.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000445 AC: 5AN: 112483Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34675
GnomAD4 exome AF: 0.0000132 AC: 14AN: 1064234Hom.: 0 Cov.: 32 AF XY: 0.0000145 AC XY: 5AN XY: 345278
GnomAD4 genome AF: 0.0000445 AC: 5AN: 112483Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34675
ClinVar
Submissions by phenotype
not provided Benign:1
SOX3: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at