9-134417178-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_002957.6(RXRA):c.631C>T(p.Arg211Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,612,266 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.631C>T | p.Arg211Cys | missense_variant | Exon 5 of 10 | ENST00000481739.2 | NP_002948.1 | |
RXRA | NM_001291920.2 | c.550C>T | p.Arg184Cys | missense_variant | Exon 5 of 10 | NP_001278849.1 | ||
RXRA | NM_001291921.2 | c.340C>T | p.Arg114Cys | missense_variant | Exon 4 of 9 | NP_001278850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.631C>T | p.Arg211Cys | missense_variant | Exon 5 of 10 | 1 | NM_002957.6 | ENSP00000419692.1 | ||
RXRA | ENST00000672570.1 | c.550C>T | p.Arg184Cys | missense_variant | Exon 5 of 10 | ENSP00000500402.1 | ||||
RXRA | ENST00000356384.4 | n.1041C>T | non_coding_transcript_exon_variant | Exon 7 of 12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460116Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726414
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.631C>T (p.R211C) alteration is located in exon 5 (coding exon 5) of the RXRA gene. This alteration results from a C to T substitution at nucleotide position 631, causing the arginine (R) at amino acid position 211 to be replaced by a cysteine (C). 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