X-140503977-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005634.3(SOX3):c.1084G>A(p.Ala362Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005634.3 missense
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: 1AN: 109252Hom.: 0 Cov.: 23 AF XY: 0.0000309 AC XY: 1AN XY: 32358 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 929037Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 284877
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000915 AC: 1AN: 109252Hom.: 0 Cov.: 23 AF XY: 0.0000309 AC XY: 1AN XY: 32358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1084G>A (p.A362T) alteration is located in exon 1 (coding exon 1) of the SOX3 gene. This alteration results from a G to A substitution at nucleotide position 1084, causing the alanine (A) at amino acid position 362 to be replaced by a threonine (T). 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