ENST00000559395.3:n.493C>T

Variant names:

• chr15-22126003-C-T
• rs1810247
• ENST00000559395.3:n.493C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000559395.3(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 ENST00000559395.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559395.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR4N3P	NR_028067.1		n.493C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR4N3P	ENST00000559395.3	TSL:6	n.493C>T		non_coding_transcript_exon	Exon 1 of 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

GnomAD2 exomes AF: 0.221 AC: 52020 AN: 235270 AF XY: 0.227

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 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

African (AFR) AF: 0.106 AC: 2389 AN: 22576

American (AMR) AF: 0.193 AC: 5666 AN: 29326

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 6132 AN: 19020

East Asian (EAS) AF: 0.320 AC: 10393 AN: 32456

South Asian (SAS) AF: 0.324 AC: 20198 AN: 62302

European-Finnish (FIN) AF: 0.292 AC: 13415 AN: 45952

Middle Eastern (MID) AF: 0.303 AC: 1124 AN: 3706

European-Non Finnish (NFE) AF: 0.295 AC: 144312 AN: 489046

Other (OTH) AF: 0.281 AC: 9811 AN: 34902

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

African (AFR) AF: 0.0939 AC: 2234 AN: 23790

American (AMR) AF: 0.171 AC: 812 AN: 4736

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 479 AN: 1822

East Asian (EAS) AF: 0.312 AC: 594 AN: 1904

South Asian (SAS) AF: 0.272 AC: 399 AN: 1466

European-Finnish (FIN) AF: 0.247 AC: 1027 AN: 4154

Middle Eastern (MID) AF: 0.170 AC: 18 AN: 106

European-Non Finnish (NFE) AF: 0.263 AC: 9004 AN: 34216

Other (OTH) AF: 0.204 AC: 182 AN: 892

Alfa AF: 0.174 Hom.: 82

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1810247; hg19: chr15-22413954;