rs12089381
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005686.3(SOX13):c.776-14T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 1,597,756 control chromosomes in the GnomAD database, including 3,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.089 ( 1055 hom., cov: 32)
Exomes 𝑓: 0.047 ( 2213 hom. )
Consequence
SOX13
NM_005686.3 intron
NM_005686.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.226
Genes affected
SOX13 (HGNC:11192): (SRY-box transcription factor 13) This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. It has also been determined to be a type-1 diabetes autoantigen, also known as islet cell antibody 12. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SOX13 | NM_005686.3 | c.776-14T>C | intron_variant | ENST00000367204.6 | NP_005677.2 | |||
SOX13 | XM_047435006.1 | c.776-14T>C | intron_variant | XP_047290962.1 | ||||
SOX13 | XM_005245623.4 | c.773-14T>C | intron_variant | XP_005245680.1 | ||||
SOX13 | XM_047435007.1 | c.773-14T>C | intron_variant | XP_047290963.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SOX13 | ENST00000367204.6 | c.776-14T>C | intron_variant | 1 | NM_005686.3 | ENSP00000356172.1 | ||||
SOX13 | ENST00000618875.4 | c.776-14T>C | intron_variant | 1 | ENSP00000478239.1 | |||||
SOX13 | ENST00000480326.1 | n.371T>C | non_coding_transcript_exon_variant | 4/6 | 5 | ENSP00000434093.1 | ||||
SOX13 | ENST00000272193.10 | n.643-14T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0891 AC: 13557AN: 152072Hom.: 1054 Cov.: 32
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GnomAD3 exomes AF: 0.0464 AC: 11457AN: 246716Hom.: 494 AF XY: 0.0442 AC XY: 5921AN XY: 134054
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GnomAD4 exome AF: 0.0466 AC: 67317AN: 1445566Hom.: 2213 Cov.: 30 AF XY: 0.0456 AC XY: 32845AN XY: 720064
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GnomAD4 genome AF: 0.0893 AC: 13583AN: 152190Hom.: 1055 Cov.: 32 AF XY: 0.0857 AC XY: 6381AN XY: 74418
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at