rs339998

chr15-60655564-C-T

Variant summary

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

The NM_134261.3(RORA):c.196+23093G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,958 control chromosomes in the GnomAD database, including 11,451 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 (11451 hom., cov: 32)
• Consequence: RORA NM_134261.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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]

LOC105370846 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RORA	NM_134261.3	c.196+23093G>A		intron_variant		ENST00000335670.11
LOC105370846	XR_007064663.1	n.8302C>T		non_coding_transcript_exon_variant	5/5
RORA	XM_011521875.3	c.139+23093G>A		intron_variant
RORA	XM_047432928.1	c.-216+21587G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RORA	ENST00000335670.11	c.196+23093G>A		intron_variant		1	NM_134261.3
	ENST00000667845.1	n.25-1794C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58456 AN: 151840 Hom.: 11447 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.385 AC: 58491 AN: 151958 Hom.: 11451 Cov.: 32 AF XY: 0.386 AC XY: 28653 AN XY: 74272

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.415

Alfa AF: 0.410 Hom.: 17413

Bravo AF: 0.387

Asia WGS AF: 0.440 AC: 1528 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.020
Dann	Benign	0.37

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: rs339998; hg19: chr15-60947763;