rs11830103
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001167856.3(SBNO1):c.651+1989T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 150,978 control chromosomes in the GnomAD database, including 6,650 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 0.27 ( 6650 hom., cov: 28)
Consequence
SBNO1
NM_001167856.3 intron
NM_001167856.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.470
Genes affected
SBNO1 (HGNC:22973): (strawberry notch homolog 1) Predicted to enable chromatin DNA binding activity and histone binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBNO1 | NM_001167856.3 | c.651+1989T>C | intron_variant | ENST00000602398.3 | |||
SBNO1 | NM_018183.5 | c.648+1989T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBNO1 | ENST00000602398.3 | c.651+1989T>C | intron_variant | 5 | NM_001167856.3 | P4 | |||
SBNO1 | ENST00000420886.6 | c.651+1989T>C | intron_variant | 1 | P4 | ||||
SBNO1 | ENST00000267176.8 | c.648+1989T>C | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.270 AC: 40675AN: 150860Hom.: 6634 Cov.: 28
GnomAD3 genomes
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28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.270 AC: 40732AN: 150978Hom.: 6650 Cov.: 28 AF XY: 0.268 AC XY: 19710AN XY: 73682
GnomAD4 genome
?
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AC:
40732
AN:
150978
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28
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19710
AN XY:
73682
Gnomad4 AFR
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442
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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