rs10483256

chr14-21669882-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317107.2(OR4E1):c.*106C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 396,224 control chromosomes in the GnomAD database, including 7,616 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 0.19 (3181 hom., cov: 32)
  • Exomes 𝑓: 0.18 (4435 hom.)
• Consequence: OR4E1 NM_001317107.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

Genes affected

OR4E1 (HGNC:8296): (olfactory receptor family 4 subfamily E member 1) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR4E1	NM_001317107.2	c.*106C>T		3_prime_UTR_variant	2/2	ENST00000641792.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR4E1	ENST00000641792.2	c.*106C>T		3_prime_UTR_variant	2/2		NM_001317107.2	P1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29590 AN: 151968 Hom.: 3185 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.179 AC: 43623 AN: 244134 Hom.: 4435 Cov.: 0 AF XY: 0.180 AC XY: 22340 AN XY: 123788

Gnomad4 AFR exome AF: 0.247

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.261

Gnomad4 EAS exome AF: 0.00981

Gnomad4 SAS exome AF: 0.0586

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.204

Gnomad4 OTH exome AF: 0.193

GnomAD4 genome AF: 0.195 AC: 29593 AN: 152090 Hom.: 3181 Cov.: 32 AF XY: 0.187 AC XY: 13899 AN XY: 74350

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.00752

Gnomad4 SAS AF: 0.0559

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.203

Alfa AF: 0.192 Hom.: 1433

Bravo AF: 0.203

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.6
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483256; hg19: chr14-22138095;