rs79233036
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000652203.1(NR1H2):c.-127-1805C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00521 in 152,292 control chromosomes in the GnomAD database, including 6 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 0.0052 ( 6 hom., cov: 32)
Consequence
NR1H2
ENST00000652203.1 intron
ENST00000652203.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.282
Genes affected
NR1H2 (HGNC:7965): (nuclear receptor subfamily 1 group H member 2) The liver X receptors, LXRA (NR1H3; MIM 602423) and LXRB, form a subfamily of the nuclear receptor superfamily and are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. The inducible LXRA is highly expressed in liver, adrenal gland, intestine, adipose tissue, macrophages, lung, and kidney, whereas LXRB is ubiquitously expressed. Ligand-activated LXRs form obligate heterodimers with retinoid X receptors (RXRs; see MIM 180245) and regulate expression of target genes containing LXR response elements (summary by Korf et al., 2009 [PubMed 19436111]).[supplied by OMIM, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BS2
High AC in GnomAd4 at 794 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1H2 | ENST00000600355.5 | c.-127-1805C>T | intron_variant | 3 | ENSP00000473099 | |||||
NR1H2 | ENST00000652203.1 | c.-127-1805C>T | intron_variant | ENSP00000499121 | P1 | |||||
NR1H2 | ENST00000593532.5 | c.-469-1321C>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000472271 |
Frequencies
GnomAD3 genomes AF: 0.00522 AC: 794AN: 152174Hom.: 6 Cov.: 32
GnomAD3 genomes
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152174
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00521 AC: 794AN: 152292Hom.: 6 Cov.: 32 AF XY: 0.00483 AC XY: 360AN XY: 74468
GnomAD4 genome
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32
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74468
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at