rs10489744

chr1-165411386-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.623-277C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,924 control chromosomes in the GnomAD database, including 25,289 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 0.55 (25289 hom., cov: 31)
• Consequence: RXRG NM_006917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RXRG	NM_006917.5	c.623-277C>T		intron_variant		ENST00000359842.10
RXRG	NM_001256570.2	c.254-277C>T		intron_variant
RXRG	NM_001256571.2	c.254-277C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXRG	ENST00000359842.10	c.623-277C>T		intron_variant		1	NM_006917.5	P1
RXRG	ENST00000619224.1	c.254-277C>T		intron_variant		1
RXRG	ENST00000470566.1	n.548-277C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83967 AN: 151806 Hom.: 25287 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.553 AC: 83997 AN: 151924 Hom.: 25289 Cov.: 31 AF XY: 0.551 AC XY: 40937 AN XY: 74254

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.589

Alfa AF: 0.635 Hom.: 15324

Bravo AF: 0.542

Asia WGS AF: 0.477 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.25
Dann	Benign	0.33

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: rs10489744; hg19: chr1-165380623;