1-204116621-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_005686.3(SOX13):c.533C>T(p.Ala178Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005686.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOX13 | NM_005686.3 | c.533C>T | p.Ala178Val | missense_variant | Exon 5 of 14 | ENST00000367204.6 | NP_005677.2 | |
SOX13 | XM_047435006.1 | c.533C>T | p.Ala178Val | missense_variant | Exon 5 of 14 | XP_047290962.1 | ||
SOX13 | XM_005245623.4 | c.533C>T | p.Ala178Val | missense_variant | Exon 5 of 14 | XP_005245680.1 | ||
SOX13 | XM_047435007.1 | c.533C>T | p.Ala178Val | missense_variant | Exon 5 of 14 | XP_047290963.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249226Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135206
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461672Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727126
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.533C>T (p.A178V) alteration is located in exon 5 (coding exon 4) of the SOX13 gene. This alteration results from a C to T substitution at nucleotide position 533, causing the alanine (A) at amino acid position 178 to be replaced by a valine (V). 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