rs1283155

Variant names:

• chr12-52045965-G-A
• rs1283155
• ENST00000478250.1:n.185+2054G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-52045965-G-A
• chr12-52045965-G-C
• chr12-52045965-G-T

Variant summary

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

The ENST00000478250.1(NR4A1):​n.185+2054G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,136 control chromosomes in the GnomAD database, including 6,141 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 0.27 (6141 hom., cov: 33)
• Consequence: NR4A1 ENST00000478250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10
• Publications: 8 publications found

Genes affected

NR4A1 (HGNC:7980): (nuclear receptor subfamily 4 group A member 1) This gene encodes a member of the steroid-thyroid hormone-retinoid receptor superfamily. Expression is induced by phytohemagglutinin in human lymphocytes and by serum stimulation of arrested fibroblasts. The encoded protein acts as a nuclear transcription factor. Translocation of the protein from the nucleus to mitochondria induces apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

ENSG00000306678 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR4A1	XM_017019248.2	c.*243G>A		3_prime_UTR_variant	Exon 4 of 4		XP_016874737.1
NR4A1	XM_017019249.2	c.*243G>A		3_prime_UTR_variant	Exon 4 of 4		XP_016874738.1
NR4A1	NM_001202234.2	c.160+4036G>A		intron_variant	Intron 2 of 7		NP_001189163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR4A1	ENST00000478250.1	n.185+2054G>A		intron_variant	Intron 1 of 1	1
NR4A1	ENST00000549102.1	n.487+2054G>A		intron_variant	Intron 1 of 1	1
NR4A1	ENST00000545748.5	c.160+4036G>A		intron_variant	Intron 2 of 7	2		ENSP00000440864.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41247 AN: 152020 Hom.: 6126 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41300 AN: 152136 Hom.: 6141 Cov.: 33 AF XY: 0.279 AC XY: 20749 AN XY: 74362

African (AFR) AF: 0.223 AC: 9265 AN: 41508

American (AMR) AF: 0.465 AC: 7111 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2032 AN: 5166

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4830

European-Finnish (FIN) AF: 0.243 AC: 2576 AN: 10588

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16601 AN: 67960

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.257 Hom.: 10526

Bravo AF: 0.290

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.44
DANN	Benign	0.76
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1283155; hg19: chr12-52439749;