11-63911944-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173587.4(RCOR2):c.1493G>A(p.Arg498His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 663,016 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R498C) has been classified as Uncertain significance.
Frequency
Consequence
NM_173587.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RCOR2 | NM_173587.4 | c.1493G>A | p.Arg498His | missense_variant | Exon 12 of 12 | ENST00000301459.5 | NP_775858.2 | |
RCOR2 | XM_047426828.1 | c.1685G>A | p.Arg562His | missense_variant | Exon 14 of 14 | XP_047282784.1 | ||
RCOR2 | NM_001363648.2 | c.1263G>A | p.Pro421Pro | synonymous_variant | Exon 11 of 11 | NP_001350577.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RCOR2 | ENST00000301459.5 | c.1493G>A | p.Arg498His | missense_variant | Exon 12 of 12 | 1 | NM_173587.4 | ENSP00000301459.4 | ||
RCOR2 | ENST00000489217.1 | n.736G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
RCOR2 | ENST00000473926.2 | n.*11G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000262 AC: 2AN: 76454Hom.: 0 Cov.: 21
GnomAD3 exomes AF: 0.0000456 AC: 2AN: 43866Hom.: 0 AF XY: 0.0000435 AC XY: 1AN XY: 22972
GnomAD4 exome AF: 0.0000273 AC: 16AN: 586562Hom.: 0 Cov.: 15 AF XY: 0.0000381 AC XY: 11AN XY: 288626
GnomAD4 genome AF: 0.0000262 AC: 2AN: 76454Hom.: 0 Cov.: 21 AF XY: 0.0000270 AC XY: 1AN XY: 37018
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1493G>A (p.R498H) alteration is located in exon 12 (coding exon 12) of the RCOR2 gene. This alteration results from a G to A substitution at nucleotide position 1493, causing the arginine (R) at amino acid position 498 to be replaced by a histidine (H). 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