ENST00000503201.1:c.-23dupC
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The ENST00000503201.1(NR3C1):c.-23dupC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 985,276 control chromosomes in the GnomAD database, including 2,059 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.063 ( 444 hom., cov: 31)
Exomes 𝑓: 0.059 ( 1615 hom. )
Consequence
NR3C1
ENST00000503201.1 5_prime_UTR
ENST00000503201.1 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.140
Publications
9 publications found
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]
NR3C1 Gene-Disease associations (from GenCC):
- glucocorticoid resistanceInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR3C1 | NR_157096.2 | n.98dupC | non_coding_transcript_exon_variant | Exon 1 of 8 | ||||
NR3C1 | NM_001364184.2 | c.-23dupC | 5_prime_UTR_variant | Exon 1 of 9 | NP_001351113.1 | |||
NR3C1 | NM_001018076.2 | c.-23dupC | 5_prime_UTR_variant | Exon 1 of 9 | NP_001018086.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR3C1 | ENST00000503201.1 | c.-23dupC | 5_prime_UTR_variant | Exon 1 of 9 | 1 | ENSP00000427672.1 | ||||
NR3C1 | ENST00000504572.5 | c.-13-3533dupC | intron_variant | Intron 2 of 9 | 1 | ENSP00000422518.1 | ||||
NR3C1 | ENST00000502892.5 | c.-14+234dupC | intron_variant | Intron 1 of 1 | 1 | ENSP00000420856.1 |
Frequencies
GnomAD3 genomes AF: 0.0633 AC: 9619AN: 151946Hom.: 442 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
9619
AN:
151946
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0589 AC: 49050AN: 833220Hom.: 1615 Cov.: 32 AF XY: 0.0585 AC XY: 22504AN XY: 384810 show subpopulations
GnomAD4 exome
AF:
AC:
49050
AN:
833220
Hom.:
Cov.:
32
AF XY:
AC XY:
22504
AN XY:
384810
show subpopulations
African (AFR)
AF:
AC:
890
AN:
15788
American (AMR)
AF:
AC:
44
AN:
984
Ashkenazi Jewish (ASJ)
AF:
AC:
178
AN:
5154
East Asian (EAS)
AF:
AC:
872
AN:
3632
South Asian (SAS)
AF:
AC:
2398
AN:
16462
European-Finnish (FIN)
AF:
AC:
11
AN:
276
Middle Eastern (MID)
AF:
AC:
128
AN:
1620
European-Non Finnish (NFE)
AF:
AC:
42572
AN:
762002
Other (OTH)
AF:
AC:
1957
AN:
27302
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
2547
5094
7642
10189
12736
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
2256
4512
6768
9024
11280
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.0633 AC: 9627AN: 152056Hom.: 444 Cov.: 31 AF XY: 0.0652 AC XY: 4844AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
9627
AN:
152056
Hom.:
Cov.:
31
AF XY:
AC XY:
4844
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
2255
AN:
41506
American (AMR)
AF:
AC:
824
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
114
AN:
3468
East Asian (EAS)
AF:
AC:
1175
AN:
5134
South Asian (SAS)
AF:
AC:
779
AN:
4810
European-Finnish (FIN)
AF:
AC:
482
AN:
10588
Middle Eastern (MID)
AF:
AC:
32
AN:
292
European-Non Finnish (NFE)
AF:
AC:
3798
AN:
67948
Other (OTH)
AF:
AC:
134
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
450
899
1349
1798
2248
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
128
256
384
512
640
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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