rs285480

Variant names:

• chr1-165434666-G-A
• rs285480
• NM_006917.5:c.50-5700C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-165434666-G-A
• chr1-165434666-G-C
• chr1-165434666-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006917.5(RXRG):​c.50-5700C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,098 control chromosomes in the GnomAD database, including 40,702 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 0.73 (40702 hom., cov: 32)
• Consequence: RXRG NM_006917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RXRG	NM_006917.5	c.50-5700C>T		intron_variant	Intron 1 of 9	ENST00000359842.10	NP_008848.1
RXRG	NM_001256570.2	c.-378-5700C>T		intron_variant	Intron 1 of 10		NP_001243499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RXRG	ENST00000359842.10	c.50-5700C>T		intron_variant	Intron 1 of 9	1	NM_006917.5	ENSP00000352900.5
RXRG	ENST00000619224.1	c.-378-5700C>T		intron_variant	Intron 1 of 10	1		ENSP00000482458.1

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110670 AN: 151980 Hom.: 40691 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.728 AC: 110732 AN: 152098 Hom.: 40702 Cov.: 32 AF XY: 0.726 AC XY: 53982 AN XY: 74344

African (AFR) AF: 0.617 AC: 25560 AN: 41450

American (AMR) AF: 0.776 AC: 11874 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2965 AN: 3470

East Asian (EAS) AF: 0.832 AC: 4300 AN: 5170

South Asian (SAS) AF: 0.693 AC: 3331 AN: 4806

European-Finnish (FIN) AF: 0.719 AC: 7620 AN: 10598

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52484 AN: 67996

Other (OTH) AF: 0.764 AC: 1611 AN: 2110

Alfa AF: 0.765 Hom.: 197091

Bravo AF: 0.730

Asia WGS AF: 0.758 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs285480; hg19: chr1-165403903;