Variant chr1-165419892-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_006917.5(RXRG):c.420C>T(p.Ala140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 1,608,642 control chromosomes in the GnomAD database, including 109,519 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 0.29 ( 7911 hom., cov: 32)

Exomes 𝑓: 0.37 ( 101608 hom. )

Consequence

RXRG
NM_006917.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.79

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP7

Synonymous conserved (PhyloP=1.79 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
RXRG	NM_006917.5 linkuse as main transcript	c.420C>T	p.Ala140=	synonymous_variant	3/10	ENST00000359842.10	NP_008848.1
RXRG	NM_001256570.2 linkuse as main transcript	c.51C>T	p.Ala17=	synonymous_variant	4/11		NP_001243499.1
RXRG	NM_001256571.2 linkuse as main transcript	c.51C>T	p.Ala17=	synonymous_variant	2/9		NP_001243500.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
RXRG	ENST00000359842.10 linkuse as main transcript	c.420C>T	p.Ala140=	synonymous_variant	3/10	1	NM_006917.5	ENSP00000352900	P1
RXRG	ENST00000619224.1 linkuse as main transcript	c.51C>T	p.Ala17=	synonymous_variant	4/11	1		ENSP00000482458
RXRG	ENST00000470566.1 linkuse as main transcript	n.345C>T		non_coding_transcript_exon_variant	2/5	3

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44604

AN:

151914

Hom.:

7907

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.302

GnomAD3 exomes

AF:

0.337

AC:

83639

AN:

247938

Hom.:

15528

AF XY:

0.349

AC XY:

46797

AN XY:

134042

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.245

Gnomad ASJ exome

AF:

0.385

Gnomad EAS exome

AF:

0.145

Gnomad SAS exome

AF:

0.350

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.396

Gnomad OTH exome

AF:

0.354

GnomAD4 exome

AF:

0.366

AC:

533521

AN:

1456610

Hom.:

101608

Cov.:

AF XY:

0.369

AC XY:

267242

AN XY:

724616

show subpopulations

Gnomad4 AFR exome

AF:

0.0960

Gnomad4 AMR exome

AF:

0.247

Gnomad4 ASJ exome

AF:

0.388

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.356

Gnomad4 FIN exome

AF:

0.466

Gnomad4 NFE exome

AF:

0.385

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.293

AC:

44613

AN:

152032

Hom.:

7911

Cov.:

AF XY:

0.296

AC XY:

22015

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.470

Gnomad4 NFE

AF:

0.389

Gnomad4 OTH

AF:

0.305

Alfa

AF:

0.366

Hom.:

24609

Bravo

AF:

0.270

Asia WGS

AF:

0.230

AC:

801

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.80

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