rs10800098

Positions:

• chr1-165439858-G-A

Variant summary

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

The NM_006917.5(RXRG):​c.49+4987C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,248 control chromosomes in the GnomAD database, including 559 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 0.062 (559 hom., cov: 33)
• Consequence: RXRG NM_006917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

RXRG (HGNC:10479): (retinoid X receptor gamma) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the antiproliferative effects of retinoic acid (RA). This receptor forms dimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene is expressed at significantly lower levels in non-small cell lung cancer cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RXRG	NM_006917.5	c.49+4987C>T		intron_variant		ENST00000359842.10	NP_008848.1
RXRG	NM_001256570.2	c.-379+4987C>T		intron_variant			NP_001243499.1
RXRG	NR_033824.2	n.283-2657C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RXRG	ENST00000359842.10	c.49+4987C>T		intron_variant		1	NM_006917.5	ENSP00000352900	P1
RXRG	ENST00000619224.1	c.-379+4987C>T		intron_variant		1		ENSP00000482458
RXRG	ENST00000465764.1	n.329-2657C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9356 AN: 152130 Hom.: 558 Cov.: 33

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0615 AC: 9370 AN: 152248 Hom.: 559 Cov.: 33 AF XY: 0.0654 AC XY: 4870 AN XY: 74456

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0899

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.0667

Gnomad4 FIN AF: 0.0635

Gnomad4 NFE AF: 0.0552

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.0606 Hom.: 824

Bravo AF: 0.0668

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.24

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: rs10800098; hg19: chr1-165409095;