rs3806855

chr5-143404564-A-Cchr5-143404564-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504572.5(NR3C1):c.-13-3712T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 961,670 control chromosomes in the GnomAD database, including 11,938 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 0.15 (1747 hom., cov: 23)
  • Exomes 𝑓: 0.16 (10191 hom.)
• Consequence: NR3C1 ENST00000504572.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779

Genes affected

NR3C1 (HGNC:7978): (nuclear receptor subfamily 3 group C member 1) This gene encodes glucocorticoid receptor, which can function both as a transcription factor that binds to glucocorticoid response elements in the promoters of glucocorticoid responsive genes to activate their transcription, and as a regulator of other transcription factors. This receptor is typically found in the cytoplasm, but upon ligand binding, is transported into the nucleus. It is involved in inflammatory responses, cellular proliferation, and differentiation in target tissues. Mutations in this gene are associated with generalized glucocorticoid resistance. Alternative splicing of this gene results in transcript variants encoding either the same or different isoforms. Additional isoforms resulting from the use of alternate in-frame translation initiation sites have also been described, and shown to be functional, displaying diverse cytoplasm-to-nucleus trafficking patterns and distinct transcriptional activities (PMID:15866175). [provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR3C1	NM_001018074.1	c.-13-3712T>G		intron_variant
NR3C1	NM_001018075.1	c.-13-3712T>G		intron_variant
NR3C1	NM_001018077.1	c.-13-3712T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR3C1	ENST00000502892.5	c.-14+55T>G		intron_variant		1
NR3C1	ENST00000504572.5	c.-13-3712T>G		intron_variant		1		P4
NR3C1	ENST00000514699.1	c.-14+586T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 21568 AN: 143000 Hom.: 1744 Cov.: 23

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0232

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.123

GnomAD4 exome AF: 0.156 AC: 127684 AN: 818580 Hom.: 10191 Cov.: 17 AF XY: 0.155 AC XY: 58797 AN XY: 378164

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.0813

Gnomad4 ASJ exome AF: 0.0636

Gnomad4 EAS exome AF: 0.0798

Gnomad4 SAS exome AF: 0.0328

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.137

GnomAD4 genome AF: 0.151 AC: 21600 AN: 143090 Hom.: 1747 Cov.: 23 AF XY: 0.150 AC XY: 10395 AN XY: 69384

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.122

Alfa AF: 0.104 Hom.: 308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	16
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806855; hg19: chr5-142784129;