9-134436587-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_002957.6(RXRA):c.1362G>A(p.Met454Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.1362G>A | p.Met454Ile | missense_variant | Exon 10 of 10 | ENST00000481739.2 | NP_002948.1 | |
RXRA | NM_001291920.2 | c.1281G>A | p.Met427Ile | missense_variant | Exon 10 of 10 | NP_001278849.1 | ||
RXRA | NM_001291921.2 | c.1071G>A | p.Met357Ile | missense_variant | Exon 9 of 9 | NP_001278850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.1362G>A | p.Met454Ile | missense_variant | Exon 10 of 10 | 1 | NM_002957.6 | ENSP00000419692.1 | ||
RXRA | ENST00000672570.1 | c.1281G>A | p.Met427Ile | missense_variant | Exon 10 of 10 | ENSP00000500402.1 | ||||
RXRA | ENST00000356384.4 | n.1772G>A | non_coding_transcript_exon_variant | Exon 12 of 12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251286Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461714Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727150
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1362G>A (p.M454I) alteration is located in exon 10 (coding exon 10) of the RXRA gene. This alteration results from a G to A substitution at nucleotide position 1362, causing the methionine (M) at amino acid position 454 to be replaced by an isoleucine (I). 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