dbSNP rs2744537: RXRB:c.*244T>G (chr6-33194438-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021976.5(RXRB):c.*244T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 492,318 control chromosomes in the GnomAD database, including 147,615 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 0.78 ( 47204 hom., cov: 33)

Exomes 𝑓: 0.76 ( 100411 hom. )

Consequence

RXRB
NM_021976.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0500

Publications

27 publications found

Variant links:

Genes affected

RXRB (HGNC:10478): (retinoid X receptor beta) This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

RXRB links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RXRB	NM_021976.5 link	c.*244T>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000374680.4	NP_068811.1	P28702-1Q5STP9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RXRB	ENST00000374680.4 link	c.*244T>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_021976.5	ENSP00000363812.3		P28702-1

Frequencies

GnomAD3 genomes

AF:

0.783

AC:

119105

AN:

152116

Hom.:

47160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.871

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.787

Gnomad ASJ

AF:

0.801

Gnomad EAS

AF:

0.972

Gnomad SAS

AF:

0.905

Gnomad FIN

AF:

0.708

Gnomad MID

AF:

0.816

Gnomad NFE

AF:

0.718

Gnomad OTH

AF:

0.799

GnomAD4 exome

AF:

0.762

AC:

259196

AN:

340084

Hom.:

100411

Cov.:

AF XY:

0.766

AC XY:

134603

AN XY:

175682

show subpopulations

African (AFR)

AF:

0.872

AC:

8480

AN:

9730

American (AMR)

AF:

0.800

AC:

9841

AN:

12306

Ashkenazi Jewish (ASJ)

AF:

0.807

AC:

9128

AN:

11318

East Asian (EAS)

AF:

0.986

AC:

25358

AN:

25722

South Asian (SAS)

AF:

0.886

AC:

19985

AN:

22566

European-Finnish (FIN)

AF:

0.703

AC:

17282

AN:

24572

Middle Eastern (MID)

AF:

0.838

AC:

1347

AN:

1608

European-Non Finnish (NFE)

AF:

0.718

AC:

151565

AN:

211114

Other (OTH)

AF:

0.767

AC:

16210

AN:

21148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2717

5433

8150

10866

13583

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

700

1400

2100

2800

3500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.783

AC:

119205

AN:

152234

Hom.:

47204

Cov.:

AF XY:

0.784

AC XY:

58373

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.871

AC:

36194

AN:

41554

American (AMR)

AF:

0.786

AC:

12032

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.801

AC:

2781

AN:

3472

East Asian (EAS)

AF:

0.972

AC:

5040

AN:

5184

South Asian (SAS)

AF:

0.905

AC:

4358

AN:

4816

European-Finnish (FIN)

AF:

0.708

AC:

7497

AN:

10594

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.718

AC:

48802

AN:

67994

Other (OTH)

AF:

0.801

AC:

1694

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1320

2640

3959

5279

6599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.754

Hom.:

53793

Bravo

AF:

0.793

Asia WGS

AF:

0.901

AC:

3130

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

0.050

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over