rs12721616

Variant names:

• chr3-119810032-C-T
• rs12721616
• NM_003889.4:c.198-29C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003889.4(NR1I2):​c.198-29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 1,613,400 control chromosomes in the GnomAD database, including 145 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 0.017 (76 hom., cov: 32)
  • Exomes 𝑓: 0.0017 (69 hom.)
• Consequence: NR1I2 NM_003889.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 4 publications found

Genes affected

NR1I2 (HGNC:7968): (nuclear receptor subfamily 1 group I member 2) This gene product belongs to the nuclear receptor superfamily, members of which are transcription factors characterized by a ligand-binding domain and a DNA-binding domain. The encoded protein is a transcriptional regulator of the cytochrome P450 gene CYP3A4, binding to the response element of the CYP3A4 promoter as a heterodimer with the 9-cis retinoic acid receptor RXR. It is activated by a range of compounds that induce CYP3A4, including dexamethasone and rifampicin. Several alternatively spliced transcripts encoding different isoforms, some of which use non-AUG (CUG) translation initiation codon, have been described for this gene. Additional transcript variants exist, however, they have not been fully characterized. [provided by RefSeq, Jul 2008]

NR1I2 Gene-Disease associations (from GenCC):

• pediatric lymphoma

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR1I2	NM_003889.4	c.198-29C>T		intron_variant	Intron 2 of 8	ENST00000393716.8	NP_003880.3
NR1I2	NM_022002.3	c.315-29C>T		intron_variant	Intron 2 of 8		NP_071285.1
NR1I2	NM_033013.3	c.198-29C>T		intron_variant	Intron 2 of 8		NP_148934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR1I2	ENST00000393716.8	c.198-29C>T		intron_variant	Intron 2 of 8	1	NM_003889.4	ENSP00000377319.3
NR1I2	ENST00000337940.4	c.315-29C>T		intron_variant	Intron 2 of 8	1		ENSP00000336528.4
NR1I2	ENST00000466380.6	c.198-29C>T		intron_variant	Intron 2 of 8	1		ENSP00000420297.2
NR1I2	ENST00000474090.1	n.486-29C>T		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0171 AC: 2608 AN: 152116 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0130

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.0148

GnomAD2 exomes AF: 0.00429 AC: 1056 AN: 246206 AF XY: 0.00308

Gnomad AFR exome AF: 0.0561

Gnomad AMR exome AF: 0.00470

Gnomad ASJ exome AF: 0.000300

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000154

Gnomad OTH exome AF: 0.00216

GnomAD4 exome AF: 0.00170 AC: 2483 AN: 1461166 Hom.: 69 Cov.: 33 AF XY: 0.00139 AC XY: 1007 AN XY: 726918

African (AFR) AF: 0.0549 AC: 1838 AN: 33468

American (AMR) AF: 0.00523 AC: 234 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.000421 AC: 11 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39692

South Asian (SAS) AF: 0.0000928 AC: 8 AN: 86252

European-Finnish (FIN) AF: 0.0000189 AC: 1 AN: 52974

Middle Eastern (MID) AF: 0.00122 AC: 7 AN: 5758

European-Non Finnish (NFE) AF: 0.000140 AC: 156 AN: 1111818

Other (OTH) AF: 0.00378 AC: 228 AN: 60368

GnomAD4 genome AF: 0.0172 AC: 2615 AN: 152234 Hom.: 76 Cov.: 32 AF XY: 0.0166 AC XY: 1233 AN XY: 74436

African (AFR) AF: 0.0572 AC: 2379 AN: 41556

American (AMR) AF: 0.0130 AC: 199 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000882 AC: 6 AN: 67994

Other (OTH) AF: 0.0147 AC: 31 AN: 2114

Alfa AF: 0.00900 Hom.: 8

Bravo AF: 0.0194

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.3
DANN	Benign	0.66
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12721616; hg19: chr3-119528879;