9-134401735-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002957.6(RXRA):c.132G>A(p.Pro44Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,613,088 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00089 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000096 ( 0 hom. )
Consequence
RXRA
NM_002957.6 synonymous
NM_002957.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.57
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-134401735-G-A is Benign according to our data. Variant chr9-134401735-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 713755.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.57 with no splicing effect.
BS2
High AC in GnomAd4 at 136 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000894 AC: 136AN: 152120Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000444 AC: 111AN: 249812Hom.: 0 AF XY: 0.000450 AC XY: 61AN XY: 135484
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GnomAD4 exome AF: 0.0000958 AC: 140AN: 1460852Hom.: 0 Cov.: 32 AF XY: 0.000100 AC XY: 73AN XY: 726762
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GnomAD4 genome AF: 0.000893 AC: 136AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.00130 AC XY: 97AN XY: 74412
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 21, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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