rs7864987

Variant summary

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

The ENST00000481739.2(RXRA):​c.28+29661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,974 control chromosomes in the GnomAD database, including 10,311 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 0.33 ( 10311 hom., cov: 32)

Consequence

RXRA
ENST00000481739.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62
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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RXRANM_002957.6 linkuse as main transcriptc.28+29661T>C intron_variant ENST00000481739.2 NP_002948.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RXRAENST00000481739.2 linkuse as main transcriptc.28+29661T>C intron_variant 1 NM_002957.6 ENSP00000419692 P3P19793-1
RXRAENST00000484822.1 linkuse as main transcriptn.452+36836T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.333
AC:
50546
AN:
151856
Hom.:
10276
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.576
Gnomad AMI
AF:
0.214
Gnomad AMR
AF:
0.240
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.219
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.250
Gnomad OTH
AF:
0.307
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.333
AC:
50637
AN:
151974
Hom.:
10311
Cov.:
32
AF XY:
0.326
AC XY:
24221
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.577
Gnomad4 AMR
AF:
0.240
Gnomad4 ASJ
AF:
0.220
Gnomad4 EAS
AF:
0.147
Gnomad4 SAS
AF:
0.271
Gnomad4 FIN
AF:
0.219
Gnomad4 NFE
AF:
0.250
Gnomad4 OTH
AF:
0.310
Alfa
AF:
0.280
Hom.:
1646
Bravo
AF:
0.345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.0
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs7864987; hg19: chr9-137248166; API