chr9-134429149-A-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002957.6(RXRA):āc.952A>Gā(p.Ile318Val) variant causes a missense change. The variant allele was found at a frequency of 0.000036 in 1,613,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00014 ( 0 hom., cov: 34)
Exomes š: 0.000025 ( 0 hom. )
Consequence
RXRA
NM_002957.6 missense
NM_002957.6 missense
Scores
8
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.16
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.13010186).
BS2
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.952A>G | p.Ile318Val | missense_variant | 7/10 | ENST00000481739.2 | |
RXRA | NM_001291920.2 | c.871A>G | p.Ile291Val | missense_variant | 7/10 | ||
RXRA | NM_001291921.2 | c.661A>G | p.Ile221Val | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.952A>G | p.Ile318Val | missense_variant | 7/10 | 1 | NM_002957.6 | P3 | |
RXRA | ENST00000672570.1 | c.871A>G | p.Ile291Val | missense_variant | 7/10 | A1 | |||
RXRA | ENST00000356384.4 | n.1362A>G | non_coding_transcript_exon_variant | 9/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152188Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250816Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135800
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GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460786Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 726728
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152306Hom.: 0 Cov.: 34 AF XY: 0.000134 AC XY: 10AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Benign
N
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at