rs10881583

chr9-134375593-T-C

Variant summary

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

The NM_002957.6(RXRA):c.29-26039T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,914 control chromosomes in the GnomAD database, including 12,912 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 0.37 (12912 hom., cov: 32)
• Consequence: RXRA NM_002957.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

RXRA (HGNC:10477): (retinoid X receptor alpha) Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RXRA	NM_002957.6	c.29-26039T>C		intron_variant		ENST00000481739.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXRA	ENST00000481739.2	c.29-26039T>C		intron_variant		1	NM_002957.6	P3
RXRA	ENST00000356384.4	n.293+1463T>C		intron_variant, non_coding_transcript_variant		5
RXRA	ENST00000484822.1	n.453-26039T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55565 AN: 151796 Hom.: 12868 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.366 AC: 55670 AN: 151914 Hom.: 12912 Cov.: 32 AF XY: 0.362 AC XY: 26849 AN XY: 74246

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.349

Alfa AF: 0.309 Hom.: 1121

Bravo AF: 0.393

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs10881583; hg19: chr9-137267439;