rs10869435

chr9-74661165-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006914.4(RORB):c.759+427T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,084 control chromosomes in the GnomAD database, including 12,281 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 0.38 (12281 hom., cov: 32)
• Consequence: RORB NM_006914.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

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]

ACMG classification

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 = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RORB	NM_006914.4	c.759+427T>A		intron_variant		ENST00000376896.8
RORB	NM_001365023.1	c.792+427T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RORB	ENST00000376896.8	c.759+427T>A		intron_variant		1	NM_006914.4	P1
RORB	ENST00000396204.2	c.792+427T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58383 AN: 151966 Hom.: 12270 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.398

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.384 AC: 58424 AN: 152084 Hom.: 12281 Cov.: 32 AF XY: 0.388 AC XY: 28804 AN XY: 74316

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.394

Alfa AF: 0.429 Hom.: 1852

Bravo AF: 0.366

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.7
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10869435; hg19: chr9-77276081;