9-74573969-G-A

Position:

• chr9-74573969-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006914.4(RORB):​c.8-56313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,130 control chromosomes in the GnomAD database, including 583 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 0.077 (583 hom., cov: 32)
• Consequence: RORB NM_006914.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RORB	NM_006914.4	c.8-56313G>A		intron_variant		ENST00000376896.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RORB	ENST00000376896.8	c.8-56313G>A		intron_variant		1	NM_006914.4	P1

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11747 AN: 152012 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0772 AC: 11743 AN: 152130 Hom.: 583 Cov.: 32 AF XY: 0.0745 AC XY: 5540 AN XY: 74352

Gnomad4 AFR AF: 0.0193

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.107 Hom.: 1300

Bravo AF: 0.0743

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	17
DANN	Benign	0.78

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: rs17612218; hg19: chr9-77188885;