rs28514894
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007121.7(NR1H2):c.182-80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,482,382 control chromosomes in the GnomAD database, including 85,765 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 10410 hom., cov: 32)
Exomes 𝑓: 0.33 ( 75355 hom. )
Consequence
NR1H2
NM_007121.7 intron
NM_007121.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.505
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 19-50378069-T-C is Benign according to our data. Variant chr19-50378069-T-C is described in ClinVar as [Benign]. Clinvar id is 1277347.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR1H2 | NM_007121.7 | c.182-80T>C | intron_variant | ENST00000253727.10 | |||
NR1H2 | NM_001256647.3 | c.181+199T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR1H2 | ENST00000253727.10 | c.182-80T>C | intron_variant | 1 | NM_007121.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.363 AC: 55159AN: 151998Hom.: 10392 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
55159
AN:
151998
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.333 AC: 442821AN: 1330266Hom.: 75355 Cov.: 23 AF XY: 0.334 AC XY: 218580AN XY: 653904
GnomAD4 exome
AF:
AC:
442821
AN:
1330266
Hom.:
Cov.:
23
AF XY:
AC XY:
218580
AN XY:
653904
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.363 AC: 55232AN: 152116Hom.: 10410 Cov.: 32 AF XY: 0.362 AC XY: 26895AN XY: 74352
GnomAD4 genome
?
AF:
AC:
55232
AN:
152116
Hom.:
Cov.:
32
AF XY:
AC XY:
26895
AN XY:
74352
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1011
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | This variant is associated with the following publications: (PMID: 20939869) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at