12-124326220-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006312.6(NCOR2):c.7334G>A(p.Arg2445His) variant causes a missense change. The variant allele was found at a frequency of 0.0000448 in 1,538,894 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R2445C) 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.7334G>A | p.Arg2445His | missense_variant | 48/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.7304G>A | p.Arg2435His | missense_variant | 47/48 | ||
NCOR2 | NM_001077261.4 | c.7166G>A | p.Arg2389His | missense_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.7334G>A | p.Arg2445His | missense_variant | 48/49 | 1 | NM_006312.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000106 AC: 15AN: 141294Hom.: 0 AF XY: 0.000145 AC XY: 11AN XY: 75816
GnomAD4 exome AF: 0.0000454 AC: 63AN: 1386640Hom.: 1 Cov.: 31 AF XY: 0.0000643 AC XY: 44AN XY: 684492
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.7334G>A (p.R2445H) alteration is located in exon 48 (coding exon 46) of the NCOR2 gene. This alteration results from a G to A substitution at nucleotide position 7334, causing the arginine (R) at amino acid position 2445 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