chr9-134436594-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_002957.6(RXRA):c.1369G>A(p.Ala457Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A457V) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.1369G>A | p.Ala457Thr | missense_variant | 10/10 | ENST00000481739.2 | |
RXRA | NM_001291920.2 | c.1288G>A | p.Ala430Thr | missense_variant | 10/10 | ||
RXRA | NM_001291921.2 | c.1078G>A | p.Ala360Thr | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.1369G>A | p.Ala457Thr | missense_variant | 10/10 | 1 | NM_002957.6 | P3 | |
RXRA | ENST00000672570.1 | c.1288G>A | p.Ala430Thr | missense_variant | 10/10 | A1 | |||
RXRA | ENST00000356384.4 | n.1779G>A | non_coding_transcript_exon_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.1369G>A (p.A457T) 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 1369, causing the alanine (A) at amino acid position 457 to be replaced by a threonine (T). 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