2-156326699-TCC-TC

Position:

• chr2-156326699-TCC-TC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006186.4(NR4A2):​c.1361+18delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.79 (47833 hom., cov: 0)
  • Exomes 𝑓: 0.77 (432389 hom.)
• Consequence: NR4A2 NM_006186.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

Genes affected

NR4A2 (HGNC:7981): (nuclear receptor subfamily 4 group A member 2) This gene encodes a member of the steroid-thyroid hormone-retinoid receptor superfamily. The encoded protein may act as a transcription factor. Mutations in this gene have been associated with disorders related to dopaminergic dysfunction, including Parkinson disease, schizophernia, and manic depression. Misregulation of this gene may be associated with rheumatoid arthritis. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR4A2	NM_006186.4	c.1361+18delG		intron_variant		ENST00000339562.9	NP_006177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NR4A2	ENST00000339562.9	c.1361+18delG		intron_variant		1	NM_006186.4	ENSP00000344479.4

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119455 AN: 151962 Hom.: 47783 Cov.: 0

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.787

GnomAD3 exomes AF: 0.715 AC: 177720 AN: 248568 Hom.: 65964 AF XY: 0.721 AC XY: 97040 AN XY: 134684

Gnomad AFR exome AF: 0.899

Gnomad AMR exome AF: 0.509

Gnomad ASJ exome AF: 0.782

Gnomad EAS exome AF: 0.434

Gnomad SAS exome AF: 0.680

Gnomad FIN exome AF: 0.793

Gnomad NFE exome AF: 0.785

Gnomad OTH exome AF: 0.750

GnomAD4 exome AF: 0.766 AC: 1117687 AN: 1459912 Hom.: 432389 Cov.: 0 AF XY: 0.763 AC XY: 554559 AN XY: 726338

Gnomad4 AFR exome AF: 0.906

Gnomad4 AMR exome AF: 0.524

Gnomad4 ASJ exome AF: 0.789

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.683

Gnomad4 FIN exome AF: 0.798

Gnomad4 NFE exome AF: 0.787

Gnomad4 OTH exome AF: 0.762

GnomAD4 genome AF: 0.786 AC: 119556 AN: 152080 Hom.: 47833 Cov.: 0 AF XY: 0.780 AC XY: 57999 AN XY: 74328

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.787

Alfa AF: 0.790 Hom.: 8647

Bravo AF: 0.776

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs35479735; hg19: chr2-157183211;