rs3782257

Variant names:

• chr12-124370357-G-A
• rs3782257
• NM_006312.6:c.2807+1665C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-124370357-G-A
• chr12-124370357-G-C
• chr12-124370357-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006312.6(NCOR2):​c.2807+1665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,074 control chromosomes in the GnomAD database, including 19,556 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (19556 hom., cov: 33)
• Consequence: NCOR2 NM_006312.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006312.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOR2	NM_006312.6	MANE Select	c.2807+1665C>T		intron	N/A	NP_006303.4
	NCOR2	NM_001206654.2		c.2753+1665C>T		intron	N/A	NP_001193583.1
	NCOR2	NM_001077261.4		c.2753+1665C>T		intron	N/A	NP_001070729.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCOR2	ENST00000405201.6	TSL:1 MANE Select	c.2807+1665C>T		intron	N/A	ENSP00000384018.1
	NCOR2	ENST00000429285.6	TSL:1	c.2753+1665C>T		intron	N/A	ENSP00000400281.2
	NCOR2	ENST00000404621.5	TSL:1	c.2753+1665C>T		intron	N/A	ENSP00000384202.1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70914 AN: 151956 Hom.: 19549 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.507

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.466 AC: 70932 AN: 152074 Hom.: 19556 Cov.: 33 AF XY: 0.465 AC XY: 34591 AN XY: 74340

African (AFR) AF: 0.182 AC: 7576 AN: 41514

American (AMR) AF: 0.579 AC: 8841 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2231 AN: 3470

East Asian (EAS) AF: 0.193 AC: 994 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5867 AN: 10580

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41279 AN: 67940

Other (OTH) AF: 0.508 AC: 1072 AN: 2112

Alfa AF: 0.561 Hom.: 85140

Bravo AF: 0.459

Asia WGS AF: 0.356 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3782257; hg19: chr12-124854903;