9-134429149-A-G
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
Consequence
NM_002957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.952A>G | p.Ile318Val | missense_variant | Exon 7 of 10 | ENST00000481739.2 | NP_002948.1 | |
RXRA | NM_001291920.2 | c.871A>G | p.Ile291Val | missense_variant | Exon 7 of 10 | NP_001278849.1 | ||
RXRA | NM_001291921.2 | c.661A>G | p.Ile221Val | missense_variant | Exon 6 of 9 | NP_001278850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.952A>G | p.Ile318Val | missense_variant | Exon 7 of 10 | 1 | NM_002957.6 | ENSP00000419692.1 | ||
RXRA | ENST00000672570.1 | c.871A>G | p.Ile291Val | missense_variant | Exon 7 of 10 | ENSP00000500402.1 | ||||
RXRA | ENST00000356384.4 | n.1362A>G | non_coding_transcript_exon_variant | Exon 9 of 12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152188Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250816Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135800
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460786Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 726728
GnomAD4 genome AF: 0.000138 AC: 21AN: 152306Hom.: 0 Cov.: 34 AF XY: 0.000134 AC XY: 10AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.952A>G (p.I318V) alteration is located in exon 7 (coding exon 7) of the RXRA gene. This alteration results from a A to G substitution at nucleotide position 952, causing the isoleucine (I) at amino acid position 318 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at