rs11749561

Positions:

• chr5-143412112-T-C

Variant summary

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

The ENST00000504572.5(NR3C1):​c.-13-11260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,828 control chromosomes in the GnomAD database, including 16,858 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 0.46 (16858 hom., cov: 30)
• Consequence: NR3C1 ENST00000504572.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR3C1	NM_001018074.1	c.-13-11260A>G		intron_variant
NR3C1	NM_001018075.1	c.-13-11260A>G		intron_variant
NR3C1	NM_001018077.1	c.-13-11260A>G		intron_variant
NR3C1	NM_001364183.2	c.-13-11260A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR3C1	ENST00000504572.5	c.-13-11260A>G		intron_variant		1		P4
NR3C1	ENST00000343796.6	c.-13-11260A>G		intron_variant		5		A1
NR3C1	ENST00000503701.1	n.353-2873A>G		intron_variant, non_coding_transcript_variant		3
NR3C1	ENST00000505058.5	n.242-2873A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69428 AN: 151708 Hom.: 16863 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.457 AC: 69445 AN: 151828 Hom.: 16858 Cov.: 30 AF XY: 0.452 AC XY: 33530 AN XY: 74182

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.469

Alfa AF: 0.518 Hom.: 23526

Bravo AF: 0.439

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.39
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11749561; hg19: chr5-142791677;