rs699699
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018013.4(SOBP):c.670-12366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 850,542 control chromosomes in the GnomAD database, including 414,078 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 0.98 ( 73019 hom., cov: 33)
Exomes 𝑓: 0.99 ( 341059 hom. )
Consequence
SOBP
NM_018013.4 intron
NM_018013.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.655
Genes affected
SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOBP | NM_018013.4 | c.670-12366G>A | intron_variant | ENST00000317357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOBP | ENST00000317357.10 | c.670-12366G>A | intron_variant | 5 | NM_018013.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.979 AC: 149018AN: 152238Hom.: 72960 Cov.: 33
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GnomAD4 exome AF: 0.988 AC: 690049AN: 698186Hom.: 341059 Cov.: 8 AF XY: 0.988 AC XY: 320803AN XY: 324582
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GnomAD4 genome ? AF: 0.979 AC: 149136AN: 152356Hom.: 73019 Cov.: 33 AF XY: 0.980 AC XY: 73035AN XY: 74506
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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