rs10482609

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000394464.7(NR3C1):​c.-325T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00846 in 985,064 control chromosomes in the GnomAD database, including 74 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 0.010 ( 21 hom., cov: 33)
Exomes 𝑓: 0.0081 ( 53 hom. )

Consequence

NR3C1
ENST00000394464.7 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.328
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0104 (1575/151716) while in subpopulation SAS AF= 0.0363 (175/4820). AF 95% confidence interval is 0.0319. There are 21 homozygotes in gnomad4. There are 832 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 21 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NR3C1NM_000176.3 linkuse as main transcriptc.-325T>G 5_prime_UTR_variant 1/9 ENST00000394464.7 NP_000167.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NR3C1ENST00000394464.7 linkuse as main transcriptc.-325T>G 5_prime_UTR_variant 1/91 NM_000176.3 ENSP00000377977 A1P04150-1

Frequencies

GnomAD3 genomes
AF:
0.0104
AC:
1572
AN:
151608
Hom.:
21
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00146
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0158
Gnomad ASJ
AF:
0.0649
Gnomad EAS
AF:
0.0220
Gnomad SAS
AF:
0.0361
Gnomad FIN
AF:
0.0128
Gnomad MID
AF:
0.0258
Gnomad NFE
AF:
0.00854
Gnomad OTH
AF:
0.0177
GnomAD4 exome
AF:
0.00811
AC:
6758
AN:
833348
Hom.:
53
Cov.:
32
AF XY:
0.00843
AC XY:
3246
AN XY:
384892
show subpopulations
Gnomad4 AFR exome
AF:
0.00146
Gnomad4 AMR exome
AF:
0.00609
Gnomad4 ASJ exome
AF:
0.0623
Gnomad4 EAS exome
AF:
0.0253
Gnomad4 SAS exome
AF:
0.0371
Gnomad4 FIN exome
AF:
0.00694
Gnomad4 NFE exome
AF:
0.00687
Gnomad4 OTH exome
AF:
0.0149
GnomAD4 genome
AF:
0.0104
AC:
1575
AN:
151716
Hom.:
21
Cov.:
33
AF XY:
0.0112
AC XY:
832
AN XY:
74142
show subpopulations
Gnomad4 AFR
AF:
0.00145
Gnomad4 AMR
AF:
0.0158
Gnomad4 ASJ
AF:
0.0649
Gnomad4 EAS
AF:
0.0221
Gnomad4 SAS
AF:
0.0363
Gnomad4 FIN
AF:
0.0128
Gnomad4 NFE
AF:
0.00854
Gnomad4 OTH
AF:
0.0185
Alfa
AF:
0.00873
Hom.:
1
Bravo
AF:
0.00997
Asia WGS
AF:
0.0450
AC:
155
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
13
DANN
Benign
0.78

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10482609; hg19: chr5-142783087; COSMIC: COSV51542047; COSMIC: COSV51542047; API