rs3832066
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_006186.4(NR4A2):c.*414_*419del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000724 in 220,902 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
NR4A2
NM_006186.4 3_prime_UTR
NM_006186.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.22
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00017 (12/70442) while in subpopulation NFE AF= 0.000245 (10/40756). AF 95% confidence interval is 0.000133. There are 0 homozygotes in gnomad4_exome. There are 6 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR4A2 | NM_006186.4 | c.*414_*419del | 3_prime_UTR_variant | 8/8 | ENST00000339562.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR4A2 | ENST00000339562.9 | c.*414_*419del | 3_prime_UTR_variant | 8/8 | 1 | NM_006186.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000266 AC: 4AN: 150460Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000170 AC: 12AN: 70442Hom.: 0 AF XY: 0.000161 AC XY: 6AN XY: 37350
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GnomAD4 genome AF: 0.0000266 AC: 4AN: 150460Hom.: 0 Cov.: 0 AF XY: 0.0000409 AC XY: 3AN XY: 73380
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at