rs6494231

Positions:

• chr15-60913793-T-C
• chr15-60913793-T-G

Variant summary

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

The NM_134261.3(RORA):​c.167-235107A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,086 control chromosomes in the GnomAD database, including 20,142 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 0.49 (20142 hom., cov: 32)
• Consequence: RORA NM_134261.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

RORA (HGNC:10258): (RAR related orphan receptor A) The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It 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, as well as with NM23-1, the product of a tumor metastasis suppressor candidate gene. Also, it has been shown to aid in the transcriptional regulation of some genes involved in circadian rhythm. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RORA	NM_134261.3	c.167-235107A>G		intron_variant		ENST00000335670.11	NP_599023.1
RORA	XM_047432928.1	c.-1751-235107A>G		intron_variant			XP_047288884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RORA	ENST00000335670.11	c.167-235107A>G		intron_variant		1	NM_134261.3	ENSP00000335087

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74990 AN: 151968 Hom.: 20146 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.493 AC: 75003 AN: 152086 Hom.: 20142 Cov.: 32 AF XY: 0.486 AC XY: 36127 AN XY: 74348

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.0559

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.505

Alfa AF: 0.580 Hom.: 36230

Bravo AF: 0.476

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.85

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: rs6494231; hg19: chr15-61205992;