rs1305047

chr17-16181671-A-AACAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006311.4(NCOR1):c.242+4882_242+4883insGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,652 control chromosomes in the GnomAD database, including 17,035 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (17035 hom., cov: 0)
• Consequence: NCOR1 NM_006311.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

NCOR1 (HGNC:7672): (nuclear receptor corepressor 1) This gene encodes a protein that mediates ligand-independent transcription repression of thyroid-hormone and retinoic-acid receptors by promoting chromatin condensation and preventing access of the transcription machinery. It is part of a complex which also includes histone deacetylases and transcriptional regulators similar to the yeast protein Sin3p. This gene is located between the Charcot-Marie-Tooth and Smith-Magenis syndrome critical regions on chromosome 17. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 17 and 20.[provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCOR1	NM_006311.4	c.242+4882_242+4883insGTGT		intron_variant		ENST00000268712.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCOR1	ENST00000268712.8	c.242+4882_242+4883insGTGT		intron_variant		1	NM_006311.4	P3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70121 AN: 151534 Hom.: 17023 Cov.: 0

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.463 AC: 70180 AN: 151652 Hom.: 17035 Cov.: 0 AF XY: 0.460 AC XY: 34089 AN XY: 74084

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.479

Alfa AF: 0.494 Hom.: 2298

Bravo AF: 0.449

Asia WGS AF: 0.252 AC: 872 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1305047; hg19: chr17-16084985;