rs6438550
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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.*758G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 985,340 control chromosomes in the GnomAD database, including 438,608 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 0.92 ( 64795 hom., cov: 32)
Exomes 𝑓: 0.95 ( 373813 hom. )
Consequence
NR1I2
NM_003889.4 3_prime_UTR
NM_003889.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.209
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1I2 | NM_003889.4 | c.*758G>A | 3_prime_UTR_variant | 9/9 | ENST00000393716.8 | ||
NR1I2 | NM_022002.3 | c.*758G>A | 3_prime_UTR_variant | 9/9 | |||
NR1I2 | NM_033013.3 | c.*758G>A | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1I2 | ENST00000393716.8 | c.*758G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_003889.4 | P2 | ||
NR1I2 | ENST00000337940.4 | c.*758G>A | 3_prime_UTR_variant | 9/9 | 1 | A2 | |||
NR1I2 | ENST00000466380.6 | c.*758G>A | 3_prime_UTR_variant | 9/9 | 1 | A2 | |||
NR1I2 | ENST00000493757.1 | n.2195G>A | non_coding_transcript_exon_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.922 AC: 140228AN: 152144Hom.: 64744 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.947 AC: 789039AN: 833078Hom.: 373813 Cov.: 26 AF XY: 0.948 AC XY: 364531AN XY: 384720
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GnomAD4 genome ? AF: 0.922 AC: 140340AN: 152262Hom.: 64795 Cov.: 32 AF XY: 0.921 AC XY: 68550AN XY: 74442
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ClinVar
Not reported inComputational scores
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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