rs55671147
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_007121.7(NR1H2):c.108G>A(p.Glu36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 1,610,756 control chromosomes in the GnomAD database, including 154 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 0.0087 ( 12 hom., cov: 32)
Exomes 𝑓: 0.014 ( 142 hom. )
Consequence
NR1H2
NM_007121.7 synonymous
NM_007121.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.645
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP7
?
Synonymous conserved (PhyloP=0.645 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00871 (1325/152206) while in subpopulation NFE AF= 0.0164 (1113/67984). AF 95% confidence interval is 0.0156. There are 12 homozygotes in gnomad4. There are 553 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1325 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1H2 | NM_007121.7 | c.108G>A | p.Glu36= | synonymous_variant | 4/10 | ENST00000253727.10 | |
NR1H2 | NM_001256647.3 | c.108G>A | p.Glu36= | synonymous_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1H2 | ENST00000253727.10 | c.108G>A | p.Glu36= | synonymous_variant | 4/10 | 1 | NM_007121.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00871 AC: 1325AN: 152088Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00943 AC: 2309AN: 244940Hom.: 20 AF XY: 0.00962 AC XY: 1281AN XY: 133116
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GnomAD4 exome AF: 0.0142 AC: 20652AN: 1458550Hom.: 142 Cov.: 32 AF XY: 0.0140 AC XY: 10152AN XY: 725594
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GnomAD4 genome ? AF: 0.00871 AC: 1325AN: 152206Hom.: 12 Cov.: 32 AF XY: 0.00743 AC XY: 553AN XY: 74412
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at