rs2076310
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021976.5(RXRB):c.640+51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,610,972 control chromosomes in the GnomAD database, including 59,525 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 0.29 ( 7039 hom., cov: 32)
Exomes 𝑓: 0.26 ( 52486 hom. )
Consequence
RXRB
NM_021976.5 intron
NM_021976.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.102
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]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRB | NM_021976.5 | c.640+51T>C | intron_variant | ENST00000374680.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRB | ENST00000374680.4 | c.640+51T>C | intron_variant | 1 | NM_021976.5 | P4 | |||
RXRB | ENST00000374685.8 | c.640+51T>C | intron_variant | 1 | A1 | ||||
RXRB | ENST00000483281.5 | c.*152+51T>C | intron_variant, NMD_transcript_variant | 5 | |||||
RXRB | ENST00000481441.1 | n.328+51T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.288 AC: 43752AN: 151954Hom.: 7012 Cov.: 32
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GnomAD3 exomes AF: 0.275 AC: 67006AN: 243888Hom.: 10927 AF XY: 0.274 AC XY: 36488AN XY: 133248
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GnomAD4 exome AF: 0.257 AC: 374562AN: 1458900Hom.: 52486 Cov.: 32 AF XY: 0.257 AC XY: 186444AN XY: 725866
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GnomAD4 genome ? AF: 0.288 AC: 43826AN: 152072Hom.: 7039 Cov.: 32 AF XY: 0.290 AC XY: 21548AN XY: 74338
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at