chr9-134409080-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 6P and 4B. PM2PP3_StrongBS2
The NM_002957.6(RXRA):c.571C>T(p.Arg191Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,454,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.571C>T | p.Arg191Cys | missense_variant | 4/10 | ENST00000481739.2 | |
RXRA | NM_001291920.2 | c.490C>T | p.Arg164Cys | missense_variant | 4/10 | ||
RXRA | NM_001291921.2 | c.280C>T | p.Arg94Cys | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.571C>T | p.Arg191Cys | missense_variant | 4/10 | 1 | NM_002957.6 | P3 | |
RXRA | ENST00000672570.1 | c.490C>T | p.Arg164Cys | missense_variant | 4/10 | A1 | |||
RXRA | ENST00000356384.4 | n.981C>T | non_coding_transcript_exon_variant | 6/12 | 5 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243724Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132170
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454362Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723446
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 25, 2023 | The c.571C>T (p.R191C) alteration is located in exon 4 (coding exon 4) of the RXRA gene. This alteration results from a C to T substitution at nucleotide position 571, causing the arginine (R) at amino acid position 191 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