rs774775666
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006312.6(NCOR2):c.5312G>A(p.Arg1771His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,494,922 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. R1771C) has been classified as Uncertain significance.
Frequency
Consequence
NM_006312.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOR2 | NM_006312.6 | c.5312G>A | p.Arg1771His | missense_variant | 37/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.5282G>A | p.Arg1761His | missense_variant | 36/48 | ||
NCOR2 | NM_001077261.4 | c.5282G>A | p.Arg1761His | missense_variant | 36/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.5312G>A | p.Arg1771His | missense_variant | 37/49 | 1 | NM_006312.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000302 AC: 4AN: 132632Hom.: 0 AF XY: 0.0000424 AC XY: 3AN XY: 70740
GnomAD4 exome AF: 0.0000112 AC: 15AN: 1342778Hom.: 0 Cov.: 35 AF XY: 0.0000122 AC XY: 8AN XY: 656812
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Dec 03, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at