rs11929668
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003889.4(NR1I2):c.1161-120C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,327,874 control chromosomes in the GnomAD database, including 14,338 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 0.13 ( 1508 hom., cov: 32)
Exomes 𝑓: 0.14 ( 12830 hom. )
Consequence
NR1I2
NM_003889.4 intron
NM_003889.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.741
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]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.1161-120C>G | intron_variant | ENST00000393716.8 | |||
NR1I2 | NM_022002.3 | c.1278-120C>G | intron_variant | ||||
NR1I2 | NM_033013.3 | c.1050-120C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.1161-120C>G | intron_variant | 1 | NM_003889.4 | P2 | |||
NR1I2 | ENST00000337940.4 | c.1278-120C>G | intron_variant | 1 | A2 | ||||
NR1I2 | ENST00000466380.6 | c.1050-120C>G | intron_variant | 1 | A2 | ||||
NR1I2 | ENST00000493757.1 | n.1293-120C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.134 AC: 20410AN: 152000Hom.: 1508 Cov.: 32
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GnomAD4 exome AF: 0.140 AC: 164509AN: 1175756Hom.: 12830 AF XY: 0.137 AC XY: 81985AN XY: 596544
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GnomAD4 genome ? AF: 0.134 AC: 20415AN: 152118Hom.: 1508 Cov.: 32 AF XY: 0.129 AC XY: 9590AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at