rs17691363
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_006914.4(RORB):c.8-12704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 152,246 control chromosomes in the GnomAD database, including 106 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 0.030 ( 106 hom., cov: 32)
Consequence
RORB
NM_006914.4 intron
NM_006914.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.69
Genes affected
RORB (HGNC:10259): (RAR related orphan receptor B) The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It is a DNA-binding protein that can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, and to help regulate the expression of some genes involved in circadian rhythm. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0302 (4593/152246) while in subpopulation NFE AF= 0.0477 (3246/68012). AF 95% confidence interval is 0.0464. There are 106 homozygotes in gnomad4. There are 2190 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4600 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RORB | NM_006914.4 | c.8-12704A>G | intron_variant | ENST00000376896.8 | |||
RORB | NM_001365023.1 | c.40+1939A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RORB | ENST00000376896.8 | c.8-12704A>G | intron_variant | 1 | NM_006914.4 | P1 | |||
RORB | ENST00000396204.2 | c.40+1939A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0302 AC: 4600AN: 152128Hom.: 108 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: 0.0302 AC: 4593AN: 152246Hom.: 106 Cov.: 32 AF XY: 0.0294 AC XY: 2190AN XY: 74438
GnomAD4 genome
?
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2190
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3478
ClinVar
Not reported inComputational scores
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Name
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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