rs10483256

Variant names:

• chr14-21669882-G-A
• rs10483256
• NM_001317107.2:c.*106C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

TRA (HGNC:12027):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR4E1	NM_001317107.2	c.*106C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000641792.2	NP_001304036.1
TRA		n.21669882G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4E1	ENST00000641792.2	c.*106C>T		3_prime_UTR_variant	Exon 2 of 2		NM_001317107.2	ENSP00000493111.1

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

African (AFR) AF: 0.247 AC: 1764 AN: 7134

American (AMR) AF: 0.151 AC: 1112 AN: 7378

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 2405 AN: 9200

East Asian (EAS) AF: 0.00981 AC: 224 AN: 22824

South Asian (SAS) AF: 0.0586 AC: 128 AN: 2186

European-Finnish (FIN) AF: 0.125 AC: 2595 AN: 20688

Middle Eastern (MID) AF: 0.187 AC: 240 AN: 1282

European-Non Finnish (NFE) AF: 0.204 AC: 32010 AN: 157166

Other (OTH) AF: 0.193 AC: 3145 AN: 16276

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

African (AFR) AF: 0.248 AC: 10277 AN: 41446

American (AMR) AF: 0.169 AC: 2580 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 890 AN: 3468

East Asian (EAS) AF: 0.00752 AC: 39 AN: 5186

South Asian (SAS) AF: 0.0559 AC: 269 AN: 4810

European-Finnish (FIN) AF: 0.122 AC: 1293 AN: 10586

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13725 AN: 67988

Other (OTH) AF: 0.203 AC: 430 AN: 2116

Alfa AF: 0.194 Hom.: 1612

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10483256; hg19: chr14-22138095;