9-134417195-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_002957.6(RXRA):c.648C>A(p.Asn216Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXRA | NM_002957.6 | c.648C>A | p.Asn216Lys | missense_variant | 5/10 | ENST00000481739.2 | |
RXRA | NM_001291920.2 | c.567C>A | p.Asn189Lys | missense_variant | 5/10 | ||
RXRA | NM_001291921.2 | c.357C>A | p.Asn119Lys | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXRA | ENST00000481739.2 | c.648C>A | p.Asn216Lys | missense_variant | 5/10 | 1 | NM_002957.6 | P3 | |
RXRA | ENST00000672570.1 | c.567C>A | p.Asn189Lys | missense_variant | 5/10 | A1 | |||
RXRA | ENST00000356384.4 | n.1058C>A | non_coding_transcript_exon_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249930Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135310
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461012Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 726826
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.648C>A (p.N216K) alteration is located in exon 5 (coding exon 5) of the RXRA gene. This alteration results from a C to A substitution at nucleotide position 648, causing the asparagine (N) at amino acid position 216 to be replaced by a lysine (K). 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