rs881657

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002957.6(RXRA):​c.28+11511A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,768 control chromosomes in the GnomAD database, including 11,979 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 0.38 ( 11979 hom., cov: 34)

Consequence

RXRA
NM_002957.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350
Variant links:
Genes affected
RXRA (HGNC:10477): (retinoid X receptor alpha) Retinoid X receptors (RXRs) and retinoic acid receptors (RARs) are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation. These receptors function as transcription factors by binding as homodimers or heterodimers to specific sequences in the promoters of target genes. The protein encoded by this gene is a member of the steroid and thyroid hormone receptor superfamily of transcriptional regulators. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RXRANM_002957.6 linkuse as main transcriptc.28+11511A>G intron_variant ENST00000481739.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RXRAENST00000481739.2 linkuse as main transcriptc.28+11511A>G intron_variant 1 NM_002957.6 P3P19793-1
RXRAENST00000484822.1 linkuse as main transcriptn.452+18686A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.377
AC:
57125
AN:
151650
Hom.:
11954
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.569
Gnomad AMI
AF:
0.223
Gnomad AMR
AF:
0.373
Gnomad ASJ
AF:
0.292
Gnomad EAS
AF:
0.215
Gnomad SAS
AF:
0.307
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.300
Gnomad OTH
AF:
0.377
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.377
AC:
57205
AN:
151768
Hom.:
11979
Cov.:
34
AF XY:
0.373
AC XY:
27668
AN XY:
74166
show subpopulations
Gnomad4 AFR
AF:
0.570
Gnomad4 AMR
AF:
0.372
Gnomad4 ASJ
AF:
0.292
Gnomad4 EAS
AF:
0.215
Gnomad4 SAS
AF:
0.307
Gnomad4 FIN
AF:
0.277
Gnomad4 NFE
AF:
0.300
Gnomad4 OTH
AF:
0.380
Alfa
AF:
0.343
Hom.:
1213
Bravo
AF:
0.396
Asia WGS
AF:
0.286
AC:
992
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.6
DANN
Benign
0.35

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.

Other links and lift over

dbSNP: rs881657; hg19: chr9-137230016; API