Variant rs2134095 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_006917.5(RXRG):c.1050C>T(p.Val350=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 1,603,440 control chromosomes in the GnomAD database, including 332,343 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: 32)

Exomes 𝑓: 0.65 ( 307054 hom. )

Consequence

RXRG
NM_006917.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Variant links:

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]

RXRG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP7

Synonymous conserved (PhyloP=-0.918 with no splicing effect.

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
RXRG	NM_006917.5 linkuse as main transcript	c.1050C>T	p.Val350=	synonymous_variant	8/10	ENST00000359842.10
RXRG	NM_001256570.2 linkuse as main transcript	c.681C>T	p.Val227=	synonymous_variant	9/11
RXRG	NM_001256571.2 linkuse as main transcript	c.681C>T	p.Val227=	synonymous_variant	7/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RXRG	ENST00000359842.10 linkuse as main transcript	c.1050C>T	p.Val350=	synonymous_variant	8/10	1	NM_006917.5	P1
RXRG	ENST00000619224.1 linkuse as main transcript	c.681C>T	p.Val227=	synonymous_variant	9/11	1

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

83971

AN:

151860

Hom.:

25287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.300

Gnomad AMI

AF:

0.684

Gnomad AMR

AF:

0.601

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.513

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.650

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.592

GnomAD3 exomes

AF:

0.614

AC:

154447

AN:

251362

Hom.:

48931

AF XY:

0.619

AC XY:

84107

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.286

Gnomad AMR exome

AF:

0.608

Gnomad ASJ exome

AF:

0.764

Gnomad EAS exome

AF:

0.534

Gnomad SAS exome

AF:

0.528

Gnomad FIN exome

AF:

0.645

Gnomad NFE exome

AF:

0.679

Gnomad OTH exome

AF:

0.640

GnomAD4 exome

AF:

0.645

AC:

936335

AN:

1451462

Hom.:

307054

Cov.:

AF XY:

0.645

AC XY:

465982

AN XY:

722886

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.605

Gnomad4 ASJ exome

AF:

0.758

Gnomad4 EAS exome

AF:

0.465

Gnomad4 SAS exome

AF:

0.531

Gnomad4 FIN exome

AF:

0.653

Gnomad4 NFE exome

AF:

0.671

Gnomad4 OTH exome

AF:

0.631

GnomAD4 genome

AF:

0.553

AC:

84000

AN:

151978

Hom.:

25289

Cov.:

AF XY:

0.551

AC XY:

40957

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.299

Gnomad4 AMR

AF:

0.601

Gnomad4 ASJ

AF:

0.752

Gnomad4 EAS

AF:

0.513

Gnomad4 SAS

AF:

0.527

Gnomad4 FIN

AF:

0.650

Gnomad4 NFE

AF:

0.672

Gnomad4 OTH

AF:

0.590

Alfa

AF:

0.652

Hom.:

74316

Bravo

AF:

0.542

EpiCase

AF:

0.686

EpiControl

AF:

0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

3.3

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over