15-22126003-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_028067.1(OR4N3P):n.493C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.20 (676 hom., cov: 10)
  • Exomes 𝑓: 0.29 (24381 hom.)
• Consequence: OR4N3P NR_028067.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

OR4N3P (HGNC:15374): (olfactory receptor family 4 subfamily N member 3 pseudogene) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR4N3P	NR_028067.1	n.493C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR4N3P	ENST00000559395.3	n.493C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 14918 AN: 73448 Hom.: 676 Cov.: 10

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.204

GnomAD3 exomes AF: 0.221 AC: 52020 AN: 235270 Hom.: 1106 AF XY: 0.227 AC XY: 28797 AN XY: 126838

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.115

Gnomad ASJ exome AF: 0.269

Gnomad EAS exome AF: 0.283

Gnomad SAS exome AF: 0.249

Gnomad FIN exome AF: 0.232

Gnomad NFE exome AF: 0.248

Gnomad OTH exome AF: 0.230

GnomAD4 exome AF: 0.289 AC: 213440 AN: 739286 Hom.: 24381 Cov.: 11 AF XY: 0.293 AC XY: 113139 AN XY: 386704

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.193

Gnomad4 ASJ exome AF: 0.322

Gnomad4 EAS exome AF: 0.320

Gnomad4 SAS exome AF: 0.324

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.295

Gnomad4 OTH exome AF: 0.281

GnomAD4 genome AF: 0.203 AC: 14914 AN: 73492 Hom.: 676 Cov.: 10 AF XY: 0.206 AC XY: 7131 AN XY: 34664

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.204

Alfa AF: 0.174 Hom.: 82

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	14
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1810247; hg19: chr15-22413954;