rs10515752
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178424.2(SOX30):c.1387+1268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,008 control chromosomes in the GnomAD database, including 2,454 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 0.17 ( 2454 hom., cov: 32)
Consequence
SOX30
NM_178424.2 intron
NM_178424.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.33
Genes affected
SOX30 (HGNC:30635): (SRY-box transcription factor 30) 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 the cell fate. The encoded protein acts as a transcriptional regulator when present in a complex with other proteins. It can activate p53 transcription to promote tumor cell apoptosis in lung cancer. The protein may be involved in the differentiation of developing male germ cells. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Apr 2015]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOX30 | NM_178424.2 | c.1387+1268C>T | intron_variant | ENST00000265007.11 | |||
SOX30 | NM_001308165.2 | c.472+1268C>T | intron_variant | ||||
SOX30 | NM_007017.3 | c.1387+1268C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOX30 | ENST00000265007.11 | c.1387+1268C>T | intron_variant | 1 | NM_178424.2 | P2 | |||
SOX30 | ENST00000311371.9 | c.1387+1268C>T | intron_variant | 1 | A2 | ||||
SOX30 | ENST00000519442.1 | c.472+1268C>T | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.167 AC: 25341AN: 151890Hom.: 2453 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.167 AC: 25361AN: 152008Hom.: 2454 Cov.: 32 AF XY: 0.166 AC XY: 12310AN XY: 74290
GnomAD4 genome
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326
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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