chr5-143399752-T-C

Position:

chr5-143399752-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000176.3(NR3C1):c.1088A>G(p.Asn363Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 1,614,126 control chromosomes in the GnomAD database, including 696 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 41 hom., cov: 32)

Exomes 𝑓: 0.028 ( 655 hom. )

Consequence

NR3C1
NM_000176.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.831

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]

NR3C1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007912159).

BP6

Variant 5-143399752-T-C is Benign according to our data. Variant chr5-143399752-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 16150.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0191 (2915/152276) while in subpopulation NFE AF= 0.033 (2243/68024). AF 95% confidence interval is 0.0318. There are 41 homozygotes in gnomad4. There are 1348 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 41 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR3C1	NM_000176.3 linkuse as main transcript	c.1088A>G	p.Asn363Ser	missense_variant	2/9	ENST00000394464.7	NP_000167.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NR3C1	ENST00000394464.7 linkuse as main transcript	c.1088A>G	p.Asn363Ser	missense_variant	2/9	1	NM_000176.3	ENSP00000377977	A1	P04150-1

Frequencies

GnomAD3 genomes

AF:

0.0192

AC:

2915

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00521

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0111

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00497

Gnomad FIN

AF:

0.0191

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0330

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.0197

AC:

4944

AN:

251480

Hom.:

AF XY:

0.0199

AC XY:

2711

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00498

Gnomad AMR exome

AF:

0.00948

Gnomad ASJ exome

AF:

0.00665

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00640

Gnomad FIN exome

AF:

0.0175

Gnomad NFE exome

AF:

0.0331

Gnomad OTH exome

AF:

0.0200

GnomAD4 exome

AF:

0.0279

AC:

40773

AN:

1461850

Hom.:

655

Cov.:

AF XY:

0.0277

AC XY:

20165

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.00421

Gnomad4 AMR exome

AF:

0.0103

Gnomad4 ASJ exome

AF:

0.00574

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00748

Gnomad4 FIN exome

AF:

0.0183

Gnomad4 NFE exome

AF:

0.0334

Gnomad4 OTH exome

AF:

0.0203

GnomAD4 genome

AF:

0.0191

AC:

2915

AN:

152276

Hom.:

Cov.:

AF XY:

0.0181

AC XY:

1348

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00520

Gnomad4 AMR

AF:

0.0111

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00518

Gnomad4 FIN

AF:

0.0191

Gnomad4 NFE

AF:

0.0330

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0293

Hom.:

Bravo

AF:

0.0180

TwinsUK

AF:

0.0302

AC:

112

ALSPAC

AF:

0.0348

AC:

134

ESP6500AA

AF:

0.00522

AC:

ESP6500EA

AF:

0.0306

AC:

263

ExAC

AF:

0.0208

AC:

2520

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0278

EpiControl

AF:

0.0274

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

GLUCOCORTICOID RECEPTOR POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Aug 01, 2007

- -

Glucocorticoid resistance

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.72

DEOGEN2

Benign

0.14

T;T;.;.;.;.;.;T

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.46

FATHMM_MKL

Benign

0.73

LIST_S2

Uncertain

0.86

.;D;D;D;.;.;D;.

MetaRNN

Benign

0.0079

T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.3

L;L;L;.;L;L;L;L

MutationTaster

Benign

0.73

D;D;D;D;N;N;N;N;N

PrimateAI

Uncertain

0.58

PROVEAN

Benign

0.090

N;N;N;N;N;N;N;N

REVEL

Benign

0.052

Sift

Benign

0.69

T;T;T;T;T;T;T;T

Sift4G

Benign

1.0

T;T;T;T;T;T;T;T

Polyphen

0.0

B;B;.;.;.;.;.;B

Vest4

0.046

MPC

0.047

ClinPred

0.0013

GERP RS

2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.031

gMVP

0.18

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over