rs2001009

Variant names:

• chr17-3117358-T-C
• rs2001009
• ENST00000575608.2:n.932T>C

Variant summary

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

The ENST00000575608.2(OR1E3):​n.932T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 300,416 control chromosomes in the GnomAD database, including 6,402 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 (5262 hom., cov: 32)
  • Exomes 𝑓: 0.088 (1140 hom.)
• Consequence: OR1E3 ENST00000575608.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

Genes affected

OR1E3 (HGNC:8191): (olfactory receptor family 1 subfamily E member 3 (gene/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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR1E3		n.3117358T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR1E3	ENST00000575608.2	n.932T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29138 AN: 152064 Hom.: 5228 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.0884 AC: 13097 AN: 148234 Hom.: 1140 Cov.: 0 AF XY: 0.0840 AC XY: 7279 AN XY: 86646

Gnomad4 AFR exome AF: 0.466

Gnomad4 AMR exome AF: 0.262

Gnomad4 ASJ exome AF: 0.0567

Gnomad4 EAS exome AF: 0.0332

Gnomad4 SAS exome AF: 0.0563

Gnomad4 FIN exome AF: 0.0545

Gnomad4 NFE exome AF: 0.0705

Gnomad4 OTH exome AF: 0.0919

GnomAD4 genome AF: 0.192 AC: 29236 AN: 152182 Hom.: 5262 Cov.: 32 AF XY: 0.189 AC XY: 14072 AN XY: 74430

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0567

Gnomad4 EAS AF: 0.0374

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.154

Alfa AF: 0.112 Hom.: 460

Bravo AF: 0.217

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001009; hg19: chr17-3020652;