chr9-134322299-A-G

Variant summary

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

The ENST00000484822.1(RXRA):​n.452+2815A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,090 control chromosomes in the GnomAD database, including 8,494 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 0.28 ( 8494 hom., cov: 33)

Consequence

RXRA
ENST00000484822.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.171
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RXRAENST00000484822.1 linkuse as main transcriptn.452+2815A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42662
AN:
151976
Hom.:
8476
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.556
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.208
Gnomad EAS
AF:
0.0664
Gnomad SAS
AF:
0.0774
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.171
Gnomad OTH
AF:
0.278
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42738
AN:
152090
Hom.:
8494
Cov.:
33
AF XY:
0.274
AC XY:
20371
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.556
Gnomad4 AMR
AF:
0.306
Gnomad4 ASJ
AF:
0.208
Gnomad4 EAS
AF:
0.0660
Gnomad4 SAS
AF:
0.0777
Gnomad4 FIN
AF:
0.112
Gnomad4 NFE
AF:
0.171
Gnomad4 OTH
AF:
0.280
Alfa
AF:
0.210
Hom.:
948
Bravo
AF:
0.313
Asia WGS
AF:
0.109
AC:
380
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.8
DANN
Benign
0.47

Splicing

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: rs4917348; hg19: chr9-137214145; API