rs10119893
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_002957.6(RXRA):c.*2344G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 152,268 control chromosomes in the GnomAD database, including 35 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 0.011 ( 35 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RXRA
NM_002957.6 3_prime_UTR
NM_002957.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.423
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).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0106 (1617/152268) while in subpopulation AFR AF= 0.0362 (1504/41556). AF 95% confidence interval is 0.0347. There are 35 homozygotes in gnomad4. There are 781 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1617 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.*2344G>A | 3_prime_UTR_variant | 10/10 | ENST00000481739.2 | ||
RXRA | NM_001291920.2 | c.*2344G>A | 3_prime_UTR_variant | 10/10 | |||
RXRA | NM_001291921.2 | c.*2344G>A | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.*2344G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_002957.6 | P3 | ||
RXRA | ENST00000356384.4 | n.4143G>A | non_coding_transcript_exon_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0106 AC: 1613AN: 152150Hom.: 35 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 102Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 82
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Data not reliable, filtered out with message: AC0;AS_VQSR
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GnomAD4 genome ? AF: 0.0106 AC: 1617AN: 152268Hom.: 35 Cov.: 33 AF XY: 0.0105 AC XY: 781AN XY: 74448
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at