chr12-124326291-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_006312.6(NCOR2):c.7263G>T(p.Gly2421=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,567,204 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0084 ( 12 hom., cov: 33)
Exomes 𝑓: 0.00082 ( 23 hom. )
Consequence
NCOR2
NM_006312.6 synonymous
NM_006312.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.795
Genes affected
NCOR2 (HGNC:7673): (nuclear receptor corepressor 2) This gene encodes a nuclear receptor co-repressor that mediates transcriptional silencing of certain target genes. The encoded protein is a member of a family of thyroid hormone- and retinoic acid receptor-associated co-repressors. This protein acts as part of a multisubunit complex which includes histone deacetylases to modify chromatin structure that prevents basal transcriptional activity of target genes. Aberrant expression of this gene is associated with certain cancers. Alternate splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Apr 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 12-124326291-C-A is Benign according to our data. Variant chr12-124326291-C-A is described in ClinVar as [Benign]. Clinvar id is 3050726.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00844 (1285/152338) while in subpopulation AFR AF= 0.0295 (1226/41568). AF 95% confidence interval is 0.0281. There are 12 homozygotes in gnomad4. There are 620 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1281 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOR2 | NM_006312.6 | c.7263G>T | p.Gly2421= | synonymous_variant | 48/49 | ENST00000405201.6 | |
NCOR2 | NM_001206654.2 | c.7233G>T | p.Gly2411= | synonymous_variant | 47/48 | ||
NCOR2 | NM_001077261.4 | c.7095G>T | p.Gly2365= | synonymous_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOR2 | ENST00000405201.6 | c.7263G>T | p.Gly2421= | synonymous_variant | 48/49 | 1 | NM_006312.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00842 AC: 1281AN: 152220Hom.: 12 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1281
AN:
152220
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00201 AC: 380AN: 188992Hom.: 6 AF XY: 0.00150 AC XY: 156AN XY: 103800
GnomAD3 exomes
AF:
AC:
380
AN:
188992
Hom.:
AF XY:
AC XY:
156
AN XY:
103800
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000821 AC: 1162AN: 1414866Hom.: 23 Cov.: 31 AF XY: 0.000682 AC XY: 478AN XY: 701340
GnomAD4 exome
AF:
AC:
1162
AN:
1414866
Hom.:
Cov.:
31
AF XY:
AC XY:
478
AN XY:
701340
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00844 AC: 1285AN: 152338Hom.: 12 Cov.: 33 AF XY: 0.00832 AC XY: 620AN XY: 74480
GnomAD4 genome
?
AF:
AC:
1285
AN:
152338
Hom.:
Cov.:
33
AF XY:
AC XY:
620
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
5
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NCOR2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 31, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -26
Find out detailed SpliceAI scores and Pangolin per-transcript scores at