rs2234960
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002957.6(RXRA):c.782C>T(p.Pro261Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00045 in 1,559,812 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002957.6 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.782C>T | p.Pro261Leu | missense_variant, splice_region_variant | 6/10 | ENST00000481739.2 | |
RXRA | NM_001291920.2 | c.701C>T | p.Pro234Leu | missense_variant, splice_region_variant | 6/10 | ||
RXRA | NM_001291921.2 | c.491C>T | p.Pro164Leu | missense_variant, splice_region_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.782C>T | p.Pro261Leu | missense_variant, splice_region_variant | 6/10 | 1 | NM_002957.6 | P3 | |
RXRA | ENST00000672570.1 | c.701C>T | p.Pro234Leu | missense_variant, splice_region_variant | 6/10 | A1 | |||
RXRA | ENST00000356384.4 | n.1192C>T | splice_region_variant, non_coding_transcript_exon_variant | 8/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000848 AC: 182AN: 214652Hom.: 1 AF XY: 0.00119 AC XY: 135AN XY: 113448
GnomAD4 exome AF: 0.000470 AC: 662AN: 1407584Hom.: 8 Cov.: 32 AF XY: 0.000686 AC XY: 475AN XY: 692084
GnomAD4 genome AF: 0.000263 AC: 40AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000323 AC XY: 24AN XY: 74414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at