rs12916023

Positions:

• chr15-61163854-A-G

Variant summary

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

The NM_134261.3(RORA):​c.166+65199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,142 control chromosomes in the GnomAD database, including 16,679 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 0.46 (16679 hom., cov: 33)
• Consequence: RORA NM_134261.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RORA	NM_134261.3	c.166+65199T>C		intron_variant		ENST00000335670.11	NP_599023.1
RORA	XM_047432928.1	c.-1752+65199T>C		intron_variant			XP_047288884.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RORA	ENST00000335670.11	c.166+65199T>C		intron_variant		1	NM_134261.3	ENSP00000335087

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70632 AN: 152024 Hom.: 16669 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.465 AC: 70672 AN: 152142 Hom.: 16679 Cov.: 33 AF XY: 0.461 AC XY: 34279 AN XY: 74364

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.452

Alfa AF: 0.472 Hom.: 4237

Bravo AF: 0.451

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.71

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: rs12916023; hg19: chr15-61456053;