9-134436595-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002957.6(RXRA):c.1370C>T(p.Ala457Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,613,914 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 (★).
Frequency
Consequence
NM_002957.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.1370C>T | p.Ala457Val | missense_variant | Exon 10 of 10 | ENST00000481739.2 | NP_002948.1 | |
RXRA | NM_001291920.2 | c.1289C>T | p.Ala430Val | missense_variant | Exon 10 of 10 | NP_001278849.1 | ||
RXRA | NM_001291921.2 | c.1079C>T | p.Ala360Val | 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.1370C>T | p.Ala457Val | missense_variant | Exon 10 of 10 | 1 | NM_002957.6 | ENSP00000419692.1 | ||
RXRA | ENST00000672570.1 | c.1289C>T | p.Ala430Val | missense_variant | Exon 10 of 10 | ENSP00000500402.1 | ||||
RXRA | ENST00000356384.4 | n.1780C>T | non_coding_transcript_exon_variant | Exon 12 of 12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251210Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135830
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461660Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727134
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1370C>T (p.A457V) alteration is located in exon 10 (coding exon 10) of the RXRA gene. This alteration results from a C to T substitution at nucleotide position 1370, causing the alanine (A) at amino acid position 457 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