rs12221497

Variant names:

• chr11-47259102-G-A
• rs12221497
• ENST00000467728.5:c.-115G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-47259102-G-A
• chr11-47259102-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000467728.5(NR1H3):​c.-115G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,591,672 control chromosomes in the GnomAD database, including 16,759 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 0.11 (1079 hom., cov: 32)
  • Exomes 𝑓: 0.14 (15680 hom.)
• Consequence: NR1H3 ENST00000467728.5 5_prime_UTR
• Scores: Splicing: ADA: 0.00003002
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 38 publications found

Genes affected

NR1H3 (HGNC:7966): (nuclear receptor subfamily 1 group H member 3) The protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily. The NR1 family members are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and intestine. It forms a heterodimer with retinoid X receptor (RXR), and regulates expression of target genes containing retinoid response elements. Studies in mice lacking this gene suggest that it may play an important role in the regulation of cholesterol homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR1H3	NM_005693.4	c.-37-78G>A		intron_variant	Intron 1 of 9	ENST00000441012.7	NP_005684.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR1H3	ENST00000441012.7	c.-37-78G>A		intron_variant	Intron 1 of 9	1	NM_005693.4	ENSP00000387946.2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16817 AN: 152172 Hom.: 1083 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.143 AC: 205133 AN: 1439382 Hom.: 15680 Cov.: 31 AF XY: 0.145 AC XY: 103506 AN XY: 713222

African (AFR) AF: 0.0559 AC: 1834 AN: 32804

American (AMR) AF: 0.0499 AC: 2134 AN: 42766

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 2230 AN: 25122

East Asian (EAS) AF: 0.0876 AC: 3435 AN: 39220

South Asian (SAS) AF: 0.226 AC: 19190 AN: 84886

European-Finnish (FIN) AF: 0.143 AC: 7532 AN: 52758

Middle Eastern (MID) AF: 0.0995 AC: 537 AN: 5396

European-Non Finnish (NFE) AF: 0.146 AC: 160168 AN: 1097172

Other (OTH) AF: 0.136 AC: 8073 AN: 59258

GnomAD4 genome AF: 0.110 AC: 16810 AN: 152290 Hom.: 1079 Cov.: 32 AF XY: 0.111 AC XY: 8259 AN XY: 74458

African (AFR) AF: 0.0575 AC: 2389 AN: 41556

American (AMR) AF: 0.0783 AC: 1197 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 323 AN: 3472

East Asian (EAS) AF: 0.0952 AC: 494 AN: 5190

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4830

European-Finnish (FIN) AF: 0.131 AC: 1389 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9618 AN: 68014

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.129 Hom.: 4448

Bravo AF: 0.0999

Asia WGS AF: 0.195 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-1.5
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000030
dbscSNV1_RF	Benign	0.0060
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12221497; hg19: chr11-47280653;