dbSNP rs2071570: NR1D1:c.-743G>T (chr17-40100837-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021724.5(NR1D1):c.-743G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 189,340 control chromosomes in the GnomAD database, including 5,926 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 0.25 ( 4988 hom., cov: 33)

Exomes 𝑓: 0.20 ( 938 hom. )

Consequence

NR1D1
NM_021724.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0830

Variant links:

Genes affected

NR1D1 (HGNC:7962): (nuclear receptor subfamily 1 group D member 1) This gene encodes a transcription factor that is a member of the nuclear receptor subfamily 1. The encoded protein is a ligand-sensitive transcription factor that negatively regulates the expression of core clock proteins. In particular this protein represses the circadian clock transcription factor aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL). This protein may also be involved in regulating genes that function in metabolic, inflammatory and cardiovascular processes. [provided by RefSeq, Jan 2013]

NR1D1 links:

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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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR1D1	NM_021724.5 link	c.-743G>T		upstream_gene_variant		ENST00000246672.4	NP_068370.1	P20393F1D8S3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR1D1	ENST00000246672.4 link	c.-743G>T		upstream_gene_variant		1	NM_021724.5	ENSP00000246672.3		P20393

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37264

AN:

152074

Hom.:

4980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.530

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.205

AC:

7614

AN:

37148

Hom.:

938

AF XY:

0.206

AC XY:

3820

AN XY:

18574

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.131

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.420

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.261

Gnomad4 NFE exome

AF:

0.181

Gnomad4 OTH exome

AF:

0.203

GnomAD4 genome

AF:

0.245

AC:

37306

AN:

152192

Hom.:

4988

Cov.:

AF XY:

0.245

AC XY:

18226

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.257

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.529

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.313

Gnomad4 NFE

AF:

0.226

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.222

Hom.:

7903

Bravo

AF:

0.238

Asia WGS

AF:

0.341

AC:

1185

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

3.1

DANN

Benign

0.79

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over