rs10482609
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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
ENST00000394464.7 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.328
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]
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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 |
---|---|---|---|---|---|---|---|---|
NR3C1 | NM_000176.3 | c.-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 |
---|---|---|---|---|---|---|---|---|---|---|
NR3C1 | ENST00000394464.7 | c.-325T>G | 5_prime_UTR_variant | 1/9 | 1 | NM_000176.3 | ENSP00000377977 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1572AN: 151608Hom.: 21 Cov.: 33
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GnomAD4 exome AF: 0.00811 AC: 6758AN: 833348Hom.: 53 Cov.: 32 AF XY: 0.00843 AC XY: 3246AN XY: 384892
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GnomAD4 genome AF: 0.0104 AC: 1575AN: 151716Hom.: 21 Cov.: 33 AF XY: 0.0112 AC XY: 832AN XY: 74142
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at